Mercurial > repos > clustalomega > clustalomega
annotate clustalomega/clustal-omega-0.2.0/README @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 |
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2 |
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3 CLUSTAL-OMEGA is a general purpose multiple sequence alignment program |
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4 for proteins. |
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5 |
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8 INTRODUCTION |
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9 |
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10 Clustal-Omega is a general purpose multiple sequence alignment (MSA) |
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11 program for proteins. It produces high quality MSAs and is capable of |
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12 handling data-sets of hundreds of thousands of sequences in reasonable |
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13 time. |
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14 |
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15 In default mode, users give a file of sequences to be aligned and |
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16 these are clustered to produce a guide tree and this is used to guide |
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17 a "progressive alignment" of the sequences. There are also facilities |
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18 for aligning existing alignments to each other, aligning a sequence to |
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19 an alignment and for using a hidden Markov model (HMM) to help guide |
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20 an alignment of new sequences that are homologous to the sequences |
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21 used to make the HMM. This latter procedure is referred to as |
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22 "external profile alignment" or EPA. |
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23 |
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24 Clustal-Omega uses HMMs for the alignment engine, based on the HHalign |
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25 package from Johannes Soeding [1]. Guide trees are optionally made |
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26 using mBed [2] which can cluster very large numbers of sequences in |
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27 O(N*log(N)) time. Multiple alignment then proceeds by aligning larger |
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28 and larger alignments using HHalign, following the clustering given by |
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29 the guide tree. |
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30 |
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31 In its current form Clustal-Omega can only align protein sequences but |
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32 not DNA/RNA sequences. It is envisioned that DNA/RNA will become |
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33 available in a future version. |
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34 |
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35 |
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36 |
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37 SEQUENCE INPUT: |
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38 |
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39 -i, --in, --infile={<file>,-} |
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40 Multiple sequence input file (- for stdin) |
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41 |
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42 --hmm-in=<file> |
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43 HMM input files |
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44 |
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45 --dealign |
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46 Dealign input sequences |
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47 |
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48 --profile1, --p1=<file> |
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49 Pre-aligned multiple sequence file (aligned columns will be kept fixed) |
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50 |
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51 --profile2, --p2=<file> |
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52 Pre-aligned multiple sequence file (aligned columns will be kept fixed) |
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53 |
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54 |
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55 For sequence and profile input Clustal-Omega uses the Squid library |
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56 from Sean Eddy [3]. |
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57 |
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58 |
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59 Clustal-Omega accepts 3 types of sequence input: (i) a sequence file |
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60 with un-aligned or aligned sequences, (ii) profiles (a multiple |
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61 alignment in a file) of aligned sequences, (iii) a HMM. Valid |
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62 combinations of the above are: |
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63 |
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64 (a) one file with un-aligned or aligned sequences (i); the sequences |
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65 will be aligned, and the alignment will be written out. For this |
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66 mode use the -i flag. If the sequences are aligned (all sequences |
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67 have the same length and at least one sequence has at least one |
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68 gap), then the alignment is turned into a HMM, the sequences are |
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69 de-aligned and the now un-aligned sequences are aligned using the |
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70 HMM as an External Profile for External Profile Alignment (EPA). |
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71 If no EPA is desired use the --dealign flag. |
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72 |
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73 Use the above option to make a multiple alignment from a set of |
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74 sequences. A sequence file must contain more than one sequence (at |
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75 least two sequences). |
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76 |
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77 (b) two profiles (ii)+(ii); the columns in each profile will be kept |
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78 fixed and the alignment of the two profiles will be written |
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79 out. Use the --p1 and --p2 flags for this mode. |
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80 |
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81 Use this option to align two alignments (profiles) together. |
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82 |
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83 (c) one file with un/aligned sequences (i) and one profile (ii); the |
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84 profile is converted into a HMM and the un-aligned sequences will |
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85 be multiply aligned (using the HMM background information) to form |
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86 a profile; this constructed profile is aligned with the input |
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87 profile; the columns in each profile (the original one and the one |
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88 created from the un-aligned sequences) will be kept fixed and the |
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89 alignment of the two profiles will be written out. Use the -i flag |
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90 in conjunction with the --p1 flag for this mode. |
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91 The un/aligned sequences file (i) must contain at least two |
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92 sequences. If a single sequence has to be aligned with a profile |
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93 the profile-profile option (b) has to be used. |
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94 |
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95 Use the above option to add new sequences to an existing |
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96 alignment. |
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97 |
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98 (d) one file with un-aligned sequences (i) and one HMM (iii); the |
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99 un-aligned sequences will be aligned to form a profile, using the |
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100 HMM as an External Profile. So far only one HMM can be input and |
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101 only HMMer2 and HMMer3 formats are allowed. The alignment will be |
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102 written out; the HMM information is discarded. As, at the moment, |
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103 only one HMM can be used, no HMM is produced if the sequences are |
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104 already aligned. Use the -i flag in conjunction with the --hmm-in |
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105 flag for this mode. Multiple HMMs can be inputted, however, in the |
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106 current version all but the first HMM will be ignored. |
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107 |
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108 Use this option to make a new multiple alignment of sequences from |
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109 the input file and use the HMM as a guide (EPA). |
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110 |
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111 |
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112 Invalid combinations of the above are: |
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113 |
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114 (v) an un/aligned sequence file containing just one sequence (i) |
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115 |
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116 (w) an un/aligned sequence file containing just one sequence and a profile |
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117 (i)+(ii) |
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118 |
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119 (x) an un/aligned sequence file containing just one sequence and a HMM |
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120 (i)+(iii) |
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121 |
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122 (y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another. |
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123 |
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124 (z) one profile (ii) cannot be aligned with a HMM (iii) |
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125 |
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126 |
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127 The following MSA file formats are allowed: |
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128 |
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129 a2m=fasta, (vienna) |
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130 clustal, |
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131 msf, |
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132 phylip, |
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133 selex, |
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134 stockholm |
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135 |
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136 |
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137 Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However, |
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138 alignment information is automatically converted into a HMM and used |
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139 during MSA, unless the --dealign flag is specifically set. Profiles |
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140 (ii) are not de-aligned. |
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141 |
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142 The Clustal-Omega alignment engine can at the moment not process |
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143 DNA/RNA. If a sequence input file (i) or a profile (ii) is interpreted |
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144 as DNA/RNA the program will terminate during the file input stage. |
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145 |
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146 |
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147 |
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148 CLUSTERING: |
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149 |
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150 --distmat-in=<file> |
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151 Pairwise distance matrix input file (skips distance computation) |
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152 |
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153 --distmat-out=<file> |
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154 Pairwise distance matrix output file |
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155 |
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156 --guidetree-in=<file> |
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157 Guide tree input file |
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158 (skips distance computation and guide tree clustering step) |
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159 |
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160 --guidetree-out=<file> |
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161 Guide tree output file |
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162 |
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163 --mbed |
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164 Fast, Mbed-like clustering for guide tree calculation |
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165 |
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166 --mbed-iter |
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167 Use Mbed-like clustering also during iteration |
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168 |
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169 |
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170 In order to produce a multiple alignment Clustal-Omega requires a |
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171 guide tree which defines the order in which sequences/profiles are |
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172 aligned. A guide tree in turn is constructed, based on a distance |
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173 matrix. Conventionally, this distance matrix is comprised of all the |
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174 pair-wise distances of the sequences. The distance measure |
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175 Clustal-Omega uses for pair-wise distances of un-aligned sequences is |
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176 the k-tuple measure [4], which was also implemented in clustal1.83 and |
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177 clustalW2 [5,6]. If the sequences inputted via -i are aligned |
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178 Clustal-Omega uses the Kimura-corrected pairwise aligned identities |
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179 [7]. The computational effort (time/memory) to calculate and store a |
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180 full distance matrix grows quadratically with the number of |
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181 sequences. Clustal-Omega can improve this scalability to N*log(N) by |
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182 employing a fast clustering algorithm called mBed [2]; this option is |
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183 invoked by specifying the --mbed flag. |
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184 |
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185 Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct |
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186 its guide trees from the distance matrix. By default, the distance |
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187 matrix is used internally to construct the guide tree and is then |
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188 discarded. By specifying --distmat-out the internal distance matrix |
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189 can be written to file. The guide trees by default are used |
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190 internally to guide the multiple alignment and are then discarded. By |
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191 specifying the --guidetree-out option these internal guide trees can |
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192 be written out to file. Conversely, the distance calculation and/or |
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193 guide tree building stage can be skipped, by reading in a |
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194 pre-calculated distance matrix and/or pre-calculated guide tree. These |
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195 options are invoked by specifying the --distmat-in and/or |
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196 --guidetree-in flags, respectively. However, distance matrix reading |
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197 is disabled in the current version. By default, distance matrix and |
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198 guide tree files are not over-written, if a file with the specified |
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199 name already exists. In this case Clustal-Omega aborts during the |
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200 command-line processing stage. To force over-writing of already |
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201 existing files use the --force flag (see MISCELLANEOUS). |
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202 |
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203 Guide trees can be iterated to refine the alignment (see section |
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204 ITERATION). Clustal-Omega takes the alignment, that was produced |
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205 initially and constructs a new distance matrix from this |
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206 alignment. The distance measure used at this stage is the Kimura |
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207 distance [7]. By default, Clustal-Omega constructs a full distance |
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208 matrix at this stage, which will then be used to create an improved |
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209 (iterated) new guide tree. To use mBed like clustering at this stage |
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210 the --mbed-iter flag has to be set. While Kimura distances in general |
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211 are much faster to calculate than k-tuple distances, time and memory |
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212 requirements still scale quadratically with the number of sequences |
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213 and mBed-type clustering should be considered for large cases. |
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214 |
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215 |
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216 |
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217 ALIGNMENT OUTPUT: |
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218 |
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219 -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout) |
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220 |
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221 --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta) |
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222 |
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223 |
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224 By default Clustal-Omega writes its results (alignments) to stdout. An |
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225 output file can be specified with the -o flag. Output to stdout is not |
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226 possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging |
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227 messages would interfere with the alignment output. By default, |
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228 alignment files are not over-written, if a file with the specified |
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229 name already exists. In this case Clustal-Omega aborts during the |
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230 command-line processing stage. To force over-writing of already |
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231 existing files use the --force flag (see MISCELLANEOUS). |
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232 |
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233 Clustal-Omega can output alignments in various formats by setting the |
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234 --outfmt flag: |
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235 |
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236 * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta |
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237 |
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238 * for Clustal format set: --outfmt=clu or --outfmt=clustal |
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239 |
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240 * for Msf format: set --outfmt= msf |
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241 |
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242 * for Phylip format set: --outfmt=phy or --outfmt=phylip |
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243 |
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244 * for Selex format set: --outfmt=selex |
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245 |
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246 * for Stockholm format set: --outfmt=st or --outfmt=stockholm |
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247 |
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248 * for Vienna format set: --outfmt=vie or --outfmt=vienna |
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249 |
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250 |
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251 ITERATION: |
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252 |
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253 --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations |
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254 |
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255 --max-guidetree-iterations=<n> Maximum guide tree iterations |
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256 |
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257 --max-hmm-iterations=<n> Maximum number of HMM iterations |
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258 |
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259 |
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260 By default, Clustal-Omega calculates (or reads in) a guide tree and |
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261 performs a multiple alignment in the order specified by this guide |
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262 tree. This alignment is then outputted. Clustal-Omega can 'iterate' |
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263 its guide tree. The hope is that the (Kimura) distances, that can be |
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264 derived from the initial alignment, will give rise to a better guide |
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265 tree, and by extension, to a better alignment. |
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266 |
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267 A similar rationale applies to HMM-iteration. MSAs in general are very |
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268 'vulnerable' at their early stages. Sequences that are aligned at an |
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269 early stage remain fixed for the rest of the MSA. Another way of |
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270 putting this is: 'once a gap, always a gap'. This behaviour can be |
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271 mitigated by HMM iteration. An initial alignment is created and turned |
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272 into a HMM. This HMM can help in a new round of MSA to 'anticipate' |
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273 where residues should align. This is using the HMM as an External |
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274 Profile and carrying out iterative EPA. In practice, individual |
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275 sequences and profiles are aligned to the External HMM, derived after |
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276 the initial alignment. Pseudo-count information is then transferred to |
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277 the (internal) HMM, corresponding to the individual |
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278 sequence/profile. The now somewhat 'softened' sequences/profiles are |
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279 then in turn aligned in the order specified by the guide |
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280 tree. Pseudo-count transfer is reduced with the size of the |
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281 profile. Individual sequences attain the greatest pseudo-count |
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282 transfer, larger profiles less so. Pseudo-count transfer to profiles |
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283 larger than, say, 10 is negligible. The effect of HMM iteration is |
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284 more pronounced in larger test sets (that is, with more sequences). |
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285 |
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286 Both, HMM- and guide tree-iteration come at a cost of increasing the |
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287 run-time. One round of guide tree iteration adds on (roughly) the time |
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288 it took to construct the initial alignment. If, for example, the |
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289 initial alignment took 1min, then it will take (roughly) 2min to |
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290 iterate the guide tree once, 3min to iterate the guide tree twice, and |
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291 so on. HMM-iteration is more costly, as each round of iteration adds |
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292 three times the time required for the alignment stage. For example, if |
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293 the initial alignment took 1min, then each additional round of HMM |
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294 iteration will add on 3min; so 4 iterations will take 13min |
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295 (=1min+4*3min). The factor of 3 stems from the fact that at every |
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296 stage both intermediate profiles have to be aligned with the |
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297 background HMM, and finally the (softened) HMMs have to be aligned as |
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298 well. All times are quoted for single processors. |
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299 |
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300 By default, guide tree iteration and HMM-iteration are coupled. This |
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301 means, at each iteration step both, guide tree and HMM, are |
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302 re-calculated. This is invoked by setting the --iter flag. For |
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303 example, if --iter=1, then first an initial alignment is produced |
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304 (without external HMM background information and using k-tuple |
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305 distances to calculate the guide tree). This initial alignment is then |
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306 used to re-calculate a new guide tree (using Kimura distances) and to |
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307 create a HMM. The new guide tree and the HMM are then used to produce |
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308 a new MSA. |
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309 |
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310 Iteration of guide tree and HMM can be de-coupled. This means that the |
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311 number of guide tree iterations and HMM iterations can be |
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312 different. This can be done by combining the --iter flag with the |
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313 --max-guidetree-iterations and/or the --max-hmm-iterations flag. The |
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314 number of guide tree iterations is the minimum of --iter and |
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315 --max-guidetree-iterations, while the number of HMM iterations is the |
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316 minimum of --iter and --max-hmm-iterations. If, for example, HMM |
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317 iteration should be performed 5 times but guide tree iteration should |
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318 be performed only 3 times, then one should set --iter=5 and |
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319 --max-guidetree-iterations=3. All three flags can be specified at the |
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320 same time (however, this makes no sense). It is not sufficient just to |
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321 specify --max-guidetree-iterations and --max-hmm-iterations but not |
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322 --iter. If any iteration is desired --iter has to be set. |
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323 |
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324 |
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325 LIMITS (will exit early, if exceeded): |
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326 |
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327 --maxnumseq=<n> Maximum allowed number of sequences |
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328 |
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329 --maxseqlen=<l> Maximum allowed sequence length |
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330 |
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331 Limits can be imposed on the number of sequences in the input file |
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332 and/or the lengths of the sequences. This cap can be set with the |
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333 --maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will |
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334 exit early, if these limits are exceeded. |
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335 |
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336 |
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337 MISCELLANEOUS: |
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338 |
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339 --auto Set options automatically (might overwrite some of your options) |
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340 |
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341 --threads=<n> Number of processors to use |
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342 |
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343 -h, --help Print help and exit |
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344 |
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345 -v, --verbose Verbose output (increases if given multiple times) |
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346 |
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347 --version Print version information and exit |
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348 |
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349 --long-version Print long version information and exit |
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350 |
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351 --force Force file overwriting |
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352 |
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353 |
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354 Users may feel unsure which options are appropriate in certain |
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355 situations. The --auto flag tries to alleviate this problem and selects |
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356 accuracy/speed flags according to the number of sequences. For less |
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357 than 1,000 sequences mBed-clustering is unnecessary and the --mbed |
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358 flag is turned off. In this case the iteration is also turned off as |
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359 the effect of iteration is more noticeable for 'larger' problems. For |
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360 1,000 to 10,000 sequences full distance matrix calculation may become |
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361 to burdensome and the --mbed flag is turned on. Iterations are set to |
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362 1 as experience has shown that accuracy can be boosted in this |
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363 regime. However, for more than 10,000 sequences iterations are turned |
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364 off again. Improvement in accuracy may be substantial, however, the |
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365 computational overhead might be too costly for average users. In this |
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366 regime the --mbed flag remains turned on as full distance matrix |
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367 calculation may become prohibitive. Expert users may want to avoid |
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368 this flag and exercise more fine tuned control by selecting the |
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369 appropriate options manually. |
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370 |
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371 Certain parts of the MSA calculation have been parallelised. Most |
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372 noticeably, the distance matrix calculation, and certain aspects of |
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373 the HMM building stage. Clustal-Omega uses OpenMP. By default, |
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374 Clustal-Omega will attempt to use as many threads as possible. For |
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375 example, on a 4-core machine Clustal-Omega will attempt to use 4 |
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376 threads. The number of threads can be limited by setting the --threads |
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377 flag. This may be desirable, for example, in the case of |
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378 benchmarking/timing. |
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379 |
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380 Help is available by specifying the -h flag. |
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381 |
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382 By default Clustal-Omega does not print any information to stdout |
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383 (other than the final alignment, if no output file is |
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384 specified). Information concerning the progress of the alignment can |
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385 be obtained by specifying one verbosity flag (-v). This may be |
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386 desirable, to verify what Clustal-Omega is actually doing at the |
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387 moment. If two verbosity flags (-v -v) are specified, command-line |
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388 flags (explicitly and implicitly set) are printed in addition to the |
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389 progress report. Triple verbose level (-v -v -v) is the most verbose |
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390 level. In addition to single- and double-verbose information much more |
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391 information is displayed: input sequences and names, details of the |
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392 tree construction and intermediate alignments. Tree construction |
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393 information includes pairwise distances. The number of pairwise |
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|
394 distances scales with the square of the number of sequences, and |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
395 double verbose mode is probably only useful for a small number of |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
396 sequences. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
397 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
398 The current version number of Clustal-Omega can be displayed by |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
399 setting the --version flag. |
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clustalomega
parents:
diff
changeset
|
400 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
401 The current version number of Clustal-Omega as well as the code-name |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
402 and the build date can be displayed by setting the --long-version |
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clustalomega
parents:
diff
changeset
|
403 flag. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
404 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
405 By default, Clustal-Omega does not over-write files. These can be (i) |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
406 alignment output, (ii) distance matrix and (iii) guide |
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clustalomega
parents:
diff
changeset
|
407 tree. Overwriting can be forced by setting the --force flag. |
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clustalomega
parents:
diff
changeset
|
408 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
409 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
410 EXAMPLES: |
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clustalomega
parents:
diff
changeset
|
411 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
412 ./clustalo -i globin.fa |
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clustalomega
parents:
diff
changeset
|
413 |
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clustalomega
parents:
diff
changeset
|
414 Clustal-Omega reads the sequence file globin.fa, aligns the sequences |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
415 and prints the result to screen in fasta/a2m format. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
416 |
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clustalomega
parents:
diff
changeset
|
417 |
ff1768533a07
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clustalomega
parents:
diff
changeset
|
418 ./clustalo -i globin.fa -o globin.sto --outfmt=st |
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clustalomega
parents:
diff
changeset
|
419 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
420 If the file globin.sto does not exist, then Clustal-Omega reads the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
421 sequence file globin.fa, aligns the sequences and prints the result to |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
422 globin.sto in Stockholm format. If the file globin.sto does exist |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
423 already, then Clustal-Omega terminates the alignment process before |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
424 reading globin.fa. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
425 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
426 |
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clustalomega
parents:
diff
changeset
|
427 ./clustalo -i globin.fa -o globin.aln --outfmt=clu --force |
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clustalomega
parents:
diff
changeset
|
428 |
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clustalomega
parents:
diff
changeset
|
429 Clustal-Omega reads the sequence file globin.fa, aligns the sequences |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
430 and prints the result to globin.aln in Clustal format, overwriting the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
431 file globin.aln, if it already exists. |
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clustalomega
parents:
diff
changeset
|
432 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
433 |
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clustalomega
parents:
diff
changeset
|
434 ./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
435 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
436 Clustal-Omega reads the sequence file globin.fa, aligns the sequences, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
437 prints the result to screen in fasta/a2m format (default), the guide |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
438 tree to globin.dnd and the distance matrix to globin.mat, overwriting |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
439 those files if they already exist. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
440 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
441 |
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clustalomega
parents:
diff
changeset
|
442 ./clustalo -i globin.fa --guidetree-in=globin.dnd |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
443 |
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clustalomega
parents:
diff
changeset
|
444 Clustal-Omega reads the files globin.fa and globin.dnd, skipping |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
445 distance calculation and guide tree creation, using instead the guide |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
446 tree specified in globin.dnd. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
447 |
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clustalomega
parents:
diff
changeset
|
448 |
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clustalomega
parents:
diff
changeset
|
449 ./clustalo -i globin.fa --hmm-in=PF00042.hmm |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
450 |
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clustalomega
parents:
diff
changeset
|
451 Clustal-Omega reads the sequence file globin.fa and the HMM file |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
452 PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
453 alignment, transferring pseudo-count information contained in |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
454 PF00042.hmm to the sequences/profiles during the MSA. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
455 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
456 |
ff1768533a07
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clustalomega
parents:
diff
changeset
|
457 ./clustalo -i globin.sto |
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clustalomega
parents:
diff
changeset
|
458 |
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clustalomega
parents:
diff
changeset
|
459 Clustal-Omega reads the file globin.sto (of aligned sequences in |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
460 Stockholm format). It converts the alignment into a HMM, de-aligns the |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
461 sequences and re-aligns them, transferring pseudo-count information to |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
462 the sequences/profiles during the MSA. The guide tree is constructed |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
463 using a full distance matrix of Kimura distances. |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
464 |
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clustalomega
parents:
diff
changeset
|
465 |
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clustalomega
parents:
diff
changeset
|
466 ./clustalo -i globin.sto --dealign |
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clustalomega
parents:
diff
changeset
|
467 |
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clustalomega
parents:
diff
changeset
|
468 Clustal-Omega reads the file globin.sto (of aligned sequences in |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
469 Stockholm format). It de-aligns the sequences and then re-aligns |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
470 them. No HMM is produced in the process, no pseudo-count information |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
471 is transferred. Consequently, the output must be the same as for |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
472 unaligned output (like in the first example ./clustalo -i globin.fa) |
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clustalomega
parents:
diff
changeset
|
473 |
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clustalomega
parents:
diff
changeset
|
474 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
475 ./clustalo -i globin.fa --iter=2 |
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clustalomega
parents:
diff
changeset
|
476 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
477 Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
478 built from k-tuple distances, and performs an initial alignment. This |
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clustalomega
parents:
diff
changeset
|
479 initial alignment is converted into a HMM and a new guide tree is |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
480 built from the Kimura distances of the initial alignment. The |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
481 un-aligned sequences are then aligned (for the second time but this |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
482 time) using pseudo-count information from the HMM created after the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
483 initial alignment (and using the new guide tree). This second |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
484 alignment is then again converted into a HMM and a new guide tree is |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
485 constructed. The un-aligned sequences are then aligned (for a third |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
486 time), again using pseudo-count information of the HMM from the |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
487 previous step and the most recent guide tree. The final alignment is |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
488 written to screen. |
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clustalomega
parents:
diff
changeset
|
489 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
490 |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
491 ./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1 |
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clustalomega
parents:
diff
changeset
|
492 |
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clustalomega
parents:
diff
changeset
|
493 Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
494 built from k-tuple distances, and performs an initial alignment. This |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
495 initial alignment is converted into a HMM and a new guide tree is |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
496 built from the Kimura distances of the initial alignment. The |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
497 un-aligned sequences are then aligned (for the second time but this |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
498 time) using pseudo-count information from the HMM created after the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
499 initial alignment (and using the new guide tree). For the last 4 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
500 iterations the guide tree is left unchanged and only HMM iteration is |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
501 performed. This means that intermediate alignments are converted to |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
502 HMMs, and these intermediate HMMs are used to guide the MSA during |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
503 subsequent iteration stages. |
ff1768533a07
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clustalomega
parents:
diff
changeset
|
504 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
505 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
506 ./clustalo -i globin.fa -o globin.a2m -v |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
507 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
508 In case the file globin.a2m does not exist, Clustal-Omega reads the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
509 file globin.fa, prints a progress report to screen and writes the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
510 alignment in (default) Fasta format to globin.a2m. The progress report |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
511 consists of the number of threads used, the number of sequences read, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
512 the current progress in the k-tuple distance calculation, completion |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
513 of the guide tree computation and current progress of the MSA stage. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
514 If the file globin.a2m already exists Clustal-Omega aborts before |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
515 reading the file globin.fa. Note that in verbose mode an output file |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
516 has to be specified, because progress/debugging information, which is |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
517 printed to screen, would interfere with the alignment being printed to |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
518 screen. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
519 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
520 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
521 ./clustalo -i PF00042_full.fa --dealign --mbed --outfmt=vie -o PF00042_full.vie --force |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
522 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
523 Clustal-Omega reads the file PF00042_full.fa. This file contains |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
524 several thousand aligned sequences. --dealign tells Clustal-Omega to |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
525 erase all alignment information and re-align the sequences from |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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526 scratch. As there are several thousand sequences calculating a full |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
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527 distance matrix may be slow. It may therefore be desirable to use the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
528 --mbed option. Clustal-Omega now will calculate pairwise distances to |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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529 a small number of reference sequences only. This will give a |
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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
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530 significant speed-up. The speed-up is greater for larger families |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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531 (more sequences). The alignment is then written out in Vienna format |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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532 (fasta format all on one line, no line breaks per sequence) to file |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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533 PF00042_full.vie. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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534 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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535 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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536 ./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
537 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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538 Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
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539 sequences (profiles). Both profiles are then aligned. The relative |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
540 positions of residues in both profiles are not changed during this |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
541 alignment, however, columns of gaps may be inserted into the profiles, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
542 respectively. The final alignment is written to file globin+pf00042.fa |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
543 in fasta format. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
544 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
545 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
546 ./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
547 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
548 Clustal-Omega reads file globin.fa of un-aligned sequences and the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
549 profile (of aligned sequences) in file PF00042_full.vie. A HMM is |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
550 created from the profile. This HMM is used to guide the alignment of |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
551 the un-aligned sequences in globin.fa. The profile that was generated |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
552 during this alignment of un-aligned globin.fa sequences is then |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
553 aligned to the input profile PF00042_full.vie. The relative positions |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
554 of residues in profile PF00042_full.vie is not changed during this |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
555 alignment, however, columns of gaps may be inserted into the |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
556 profile. The final alignment is output to file pf00042+globin.fa in |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
557 fasta format. The alignment in this example may be slightly different |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
558 from the alignment in the previous example, because no HMM guidance |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
559 was used generate the profile globin.sto. In this example HMM guidance |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
560 was used to align the sequences in globin.fa; the hope being that this |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
561 intermediate alignment will have profited from the bigger profile. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
562 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
563 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
564 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
565 LITERATURE: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
566 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
567 [1] Johannes Soding (2005) Protein homology detection by HMM-HMM |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
568 comparison. Bioinformatics 21 (7): 951–960. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
569 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
570 [2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
571 embedding for fast construction of guide trees for multiple |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
572 sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
573 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
574 [3] http://www.genetics.wustl.edu/eddy/software/#squid |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
575 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
576 [4] Wilbur and Lipman, 1983; PMID 6572363 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
577 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
578 [5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
579 the sensitivity of progressive multiple sequence alignment through |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
580 sequence weighting, position-specific gap penalties and weight |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
581 matrix choice. Nucleic Acids Res., 22, 4673-4680. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
582 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
583 [6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
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|
584 McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
585 Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
586 2.0. Bioinformatics, 23, 2947-2948. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
587 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
588 [7] Kimura M (1980). "A simple method for estimating evolutionary |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
589 rates of base substitutions through comparative studies of |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
590 nucleotide sequences". Journal of Molecular Evolution 16: 111–120. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
591 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
592 [8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
593 accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
594 |