Repository 'fasttree_linux_64bit'
hg clone https://toolshed.g2.bx.psu.edu/repos/qfab/fasttree_linux_64bit

Changeset 0:b2b9795cc862 (2014-05-29)
Next changeset 1:3641b4766e1e (2014-05-29)
Commit message:
Uploaded
added:
fasttree/.fasttree.xml.swp
fasttree/README.txt
fasttree/fasttree.xml
fasttree/test-data/aligned.fasta
fasttree/test-data/log.txt
fasttree/test-data/tree.nhx
fasttree/tool_dependencies.xml
b
diff -r 000000000000 -r b2b9795cc862 fasttree/.fasttree.xml.swp
b
Binary file fasttree/.fasttree.xml.swp has changed
b
diff -r 000000000000 -r b2b9795cc862 fasttree/README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/README.txt Thu May 29 23:53:21 2014 -0400
b
@@ -0,0 +1,40 @@
+Galaxy wrappers for FastTree for Linux 64-bit
+================================================================================
+
+FastTree infers approximately-maximum-likelihood phylogenetic trees from
+alignments of nucleotide or protein sequences. FastTree can handle alignments
+with up to a million of sequences in a reasonable amount of time and memory.
+For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or
+RAxML 7. FastTree is open-source software.
+
+
+Installation
+================================================================================
+
+Galaxy will automatically install the required dependencies:
+- FastTree v2.1.7
+
+Please note, this FastTree v2.1.7 executable is just intended for Linux 64-bit!
+
+
+Disclaimer
+================================================================================
+
+This source code is provided by QFAB Bioinformatics "as is", in the hope
+that it will be useful, and any express or implied warranties, including,
+but not limited to, the implied warranties of merchantability and fitness
+for a particular purpose are disclaimed.
+IN NO EVENT SHALL QFAB BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT(INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOURCE
+CODE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+License
+================================================================================
+
+This work by QFAB Bioinformatics (as part of the GVL project http://genome.edu.au)
+is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0
+International License.
+                        
b
diff -r 000000000000 -r b2b9795cc862 fasttree/fasttree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/fasttree.xml Thu May 29 23:53:21 2014 -0400
b
@@ -0,0 +1,100 @@
+<tool name="FastTree" id="fasttree" version="2.17"> 
+<description>FastTree - FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</description>
+ <command>
+ FastTree $format &lt; $input &gt; $output 2&gt; $log
+</command>
+ <requirements>
+    <requirement type="package" version="2.17">FastTree</requirement>
+  </requirements>
+ <inputs>
+  <param name="input" type="data" format="fasta" label="Aligned sequences file (FASTA format)" help="Aligment, e.g. from the 'PyNAST' tool"/>
+  <param name="format" type="select" label="Nucleotide or protein alignment" help="Specify if the aligned sequences are nucleotide or protein sequences">
+        <option value="-nt" selected="true">Nucleotide</option>
+        <option value="">Protein</option>
+  </param>
+</inputs>
+<outputs>
+  <data name="output" format="nhx" type="nhx" label="${tool.name} on ${on_string}:tree.nhx" />
+  <data name="log" format="txt" hidden="TRUE" type="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt" />
+</outputs>
+<tests>
+  <test>
+    <param name="input_file" value="seq.fna" />
+    <param name="mode" value="-nt" />
+    <output name="output" file="tree.nhx" ftype="txt" lines_diff="10" />
+    <output name="log" file="log_FastTree_run.txt" ftype="txt" lines_diff="10" />
+  </test>
+</tests>
+<help>
+===========
+Description
+===========
+
+.. class:: infomark
+
+An additional file is generated by this tool, which is hidden from the history list. You can view these outputs by clicking on the cogwheel next to the "History Panel" and select "Include Hidden Dataset".
+
+FastTree_ infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software.
+
+.. _FastTree: http://meta.microbesonline.org/fasttree
+
+-----
+
+-----
+Input
+-----
+
+A) Aligned sequences file in FASTA format, e.g. the alignment from the 'PyNAST' tool.
+
+----------
+Parameters
+----------
+
+Nucleotide or protein alignment
+ To specify the type of sequence alignment (nucleotide or protein) you are providing.
+
+------
+Output
+------
+
+This tool produces two output files, one of which is hidden by default (the log file).
+
+.. class:: infomark
+
+You can view the hidden output by clicking on the cog wheel next to the History panel and select "Include Hidden Dataset".
+
+(A) The phylogenetic tree in Newick_ format (nhx).
+
+.. class:: infomark
+
+ The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences.
+
+(B) *(hidden)* The log file, containing information of the FastTree run to build the phylogenetic tree. 
+
+
+.. _Newick: http://en.wikipedia.org/wiki/Newick_format
+
+-----
+
+
+=========
+Resources
+=========
+
+FastTree_
+
+.. _FastTree: http://meta.microbesonline.org/fasttree/#Install
+
+**Wrapper Author**
+
+QFAB Bioinformatics (support@qfab.org)
+</help>
+<tests>
+  <test>
+    <param name="input" value="aligned.fasta" />
+    <param name="format" value="-nt" />
+    <output name="output" file="tree.nhx" ftype="nhx" lines_diff="10" />
+    <output name="log" file="log.txt" ftype="txt" lines_diff="10" />
+  </test>
+</tests>
+</tool>
b
diff -r 000000000000 -r b2b9795cc862 fasttree/test-data/aligned.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/test-data/aligned.fasta Thu May 29 23:53:21 2014 -0400
b
b'@@ -0,0 +1,1066 @@\n+>248442;size=4; 15..1500\n+---------------------------------------------------------------------------------------------------------------------------------GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CGC----------------G-A------------------------------AA-T-CT----------------------------------------------------CCTTC---------------------------------------------------------------------------------GGGA-GT--------------------GA--G--TA--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-GC-G-T-A-GG---A-A--T-CT-A--C-C-CAG--TG-G------------------------------------------------------------------T-GG----GGG-AC-AA-CCT-------------------------G-G-G-----------------------GAA-A---CCC-AGG-CTAA-TA---CC-G--C-AT-A----------C--------------------G-------------------------------------CC------------------------------------------------------------------------------------------------------------------------CT-AC-G--------------------------------------------------------------------------------------------------------------------------------------G-G-G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-C-G-GG-----G--GC-T--C-----------------------------------------------------------------------------------------------------------------TCTTCGGA----------------------------------------------------------------------------------------------------------------------G-A--CC-TC--G---C-G--------------C----C-A---T-TG-G---AT---G-A-----G-CCT-GCG--T-TGG--A------TT--A--G-CT-A----G---TTGG-T-G-GG-G-T----AAA-GG-C-C-T-ACCA--A-GG-C-G--A-CG-A------------TCC-A-T------AG-CT-G-G-TCT-G-AG----A--GG-AC--G-AT-C-AG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCG-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-CG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CT-----CT-AG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--T-AGG----GA-G--A---AA-AAGC---TCAT-GT----T--T--AA-T---A----G-----AT-G-TGA-GTG-TT-GA-TG-TT-A-C-CT-A-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-GC--G-TA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-G---G-ATG-TG-A-AA-GC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-T----T-G-C-A-T-T--------C--GA-T-A-C-T-G-ATC--G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-A-----C-GA--GA-G-A------------G-GG-A-GG-T----AG--AATT-CCA-C-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-A-TG-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-TCCTG------G-CT-CG-----------------------------------------------'..b'-------------------------------------T-TG--A-G-G-A-----T-GC--GA-G-A------------G-GA-A-AG-C----GG--AACT-CAT-A-GT--GT-A-GCG-GTGAAA-TG-CGT-TGAT-A-TT-A-TGG--GG-A-AC-A-CC-AA--A--T--GC-GAA-G--G-C---A----G--C-T-TTCTG------G-AG-CA---------------------------------------------------------------T-C-C-T--GA--CA-----CT-GA-AA--C-A-CGA--AA-G-C--------------G-TGGG-TAG-C-G-AACG--GG-ATTA-G-ATA-C-----CC-C-G-GTA-G-T----C-CA--C-G-CCC-T-AAA--CG-ATG-AT--CA-CT---------A-GC--T--A-T-TC-G-GA-G----------------------------------------------------------------------------------------TATC-GA-C--------------------------------------------------------------------------------------------------------------------------------------------------C-T-CC--A-A-G-T-GG-C------GT--A----GC-TAA--CG-C-G-T--T--AA-GT--G----A-TCC-GCC-T-G-GG-TAG-TA---CGG-----C-C--G-C-A-A-GGC-T--AAA-ACTC-AAA---------GGAA-TAG-ACGGG-G-A-CTTG----C-A--C-A-A-GCG-GA-G--G--AA-CA-T--GT-GGT-TC-AATT-C-G-ATG-GTAA-A-CGAA-A--A-A-CC-TT-A-CC-AGGGT-TG-G-AA-A-T--------------C-AGT-T-G-----------A-G-A--T-A-G--GC--A-GA---A-A--C-G-T--C-T-A-------------T-------------------------------------G--CC-----------------------------------------GCAAG-----G-------CA-ATT---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-TC--GTC-GTC-A-GT-TC---G-TG-GC-T--TGA-GT-TGT-T-CC-C-TT-CA-GT-GGGGT-AA--------C-GAA-CGC-A-ACC-C-C-CG--TT--G-CCTG--G-T-A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-T--AT---------------C-A-G-G-C-GA-G--AC-T-G-CCC-AG-G------------------------------------T-T---AA-----------------------------------C-T-G-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GCC--AGAT-C---AGC-A-T-G-G-C-C---CTT--AT-A--CC-T-G-GG-CC-TA-CAC-ACGTG-T--TA--CAATG---G-CCGA-C-T--C-A-C-GC-G--------------------------------------------------------------------------------------------------AG-G-C-G-A--A-GAGG-A--A---------------------------------------A-CT-C-G-----------G--A-G-CA---A----------A--TCG--------T---AAAAAGTC-G-G-C-C-AAG-TTC--------GGA-T-TGAGG-GC--T-GCAA-C-TC-------------------------------------------------------------------------------------------------G-CCCTC-A-T-G-AA-G-CG-GGATT-CG-C-TA--G-TA-AT-C-G-C----AGA-TC-A-G-C-------AT--GCT-GC-G-GT-G-AAT-ACGT-T-CTCAAGTCT-TGTA----CTCACCG-CCC-GTC-----A---AC--TCA-AG-GG-A--G---CTG-G-GA-AT-ACC--C-GAA------G--T-CGC-C--C-------------------------------------------------------------------------TT---------------------------------------------------------------------------------------------------------------------------GG-GCG--CC-TAAG-G----T-AAG-CT-CAG------------------------TG--ACA-GGGA-GT-AAG-TCGTAACAA-GGTAA-CC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n'
b
diff -r 000000000000 -r b2b9795cc862 fasttree/test-data/log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/test-data/log.txt Thu May 29 23:53:21 2014 -0400
b
b'@@ -0,0 +1,147 @@\n+FastTree Version 2.1.7 SSE3\n+Alignment: standard input\n+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000\n+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1\n+TopHits: 1.00*sqrtN close=default refresh=0.80\n+ML Model: Jukes-Cantor, CAT approximation with 20 rate categories\n+Ignored unknown character K (seen 1 times)\n+Ignored unknown character R (seen 4 times)\n+Ignored unknown character S (seen 5 times)\n+Ignored unknown character X (seen 240 times)\n+Ignored unknown character Y (seen 2 times)\n+      1.46 seconds: Top hits for    399 of    533 seqs (at seed    200)\n+      1.69 seconds: Top hits for    459 of    533 seqs (at seed    300)\n+      1.87 seconds: Top hits for    498 of    533 seqs (at seed    400)\n+      2.06 seconds: Top hits for    526 of    533 seqs (at seed    500)\n+      3.31 seconds: Joined    100 of    530\n+      4.88 seconds: Joined    200 of    530\n+      6.11 seconds: Joined    300 of    530\n+      7.43 seconds: Joined    400 of    530\n+      8.67 seconds: Joined    500 of    530\n+Initial topology in 8.86 seconds\n+Refining topology: 36 rounds ME-NNIs, 2 rounds ME-SPRs, 18 rounds ML-NNIs\n+      8.86 seconds: ME NNI round 1 of 36, 1 of 531 splits\n+      9.05 seconds: ME NNI round 1 of 36, 201 of 531 splits, 40 changes (max delta 0.029)\n+      9.23 seconds: ME NNI round 1 of 36, 401 of 531 splits, 71 changes (max delta 0.029)\n+      9.36 seconds: ME NNI round 2 of 36, 1 of 531 splits\n+      9.54 seconds: ME NNI round 2 of 36, 201 of 531 splits, 19 changes (max delta 0.013)\n+      9.73 seconds: ME NNI round 2 of 36, 401 of 531 splits, 40 changes (max delta 0.016)\n+      9.85 seconds: ME NNI round 3 of 36, 1 of 531 splits\n+     10.04 seconds: ME NNI round 3 of 36, 201 of 531 splits, 17 changes (max delta 0.003)\n+     10.19 seconds: ME NNI round 4 of 36, 1 of 531 splits\n+     10.38 seconds: ME NNI round 4 of 36, 201 of 531 splits, 10 changes (max delta 0.005)\n+     10.52 seconds: ME NNI round 5 of 36, 101 of 531 splits, 5 changes (max delta 0.003)\n+     10.65 seconds: SPR round   1 of   2, 1 of 1064 nodes\n+     12.20 seconds: SPR round   1 of   2, 101 of 1064 nodes\n+     13.72 seconds: SPR round   1 of   2, 201 of 1064 nodes\n+     15.33 seconds: SPR round   1 of   2, 301 of 1064 nodes\n+     16.82 seconds: SPR round   1 of   2, 401 of 1064 nodes\n+     18.48 seconds: SPR round   1 of   2, 501 of 1064 nodes\n+     19.91 seconds: SPR round   1 of   2, 601 of 1064 nodes\n+     21.36 seconds: SPR round   1 of   2, 701 of 1064 nodes\n+     23.06 seconds: SPR round   1 of   2, 801 of 1064 nodes\n+     24.59 seconds: SPR round   1 of   2, 901 of 1064 nodes\n+     26.04 seconds: SPR round   1 of   2, 1001 of 1064 nodes\n+     27.28 seconds: ME NNI round 13 of 36, 1 of 531 splits\n+     27.46 seconds: ME NNI round 13 of 36, 201 of 531 splits, 1 changes (max delta 0.007)\n+     27.64 seconds: ME NNI round 13 of 36, 401 of 531 splits, 2 changes (max delta 0.007)\n+     27.76 seconds: ME NNI round 14 of 36, 1 of 531 splits\n+     27.94 seconds: ME NNI round 14 of 36, 201 of 531 splits, 1 changes (max delta 0.003)\n+     28.11 seconds: ME NNI round 14 of 36, 401 of 531 splits, 1 changes (max delta 0.003)\n+     28.23 seconds: ME NNI round 15 of 36, 1 of 531 splits\n+     29.84 seconds: SPR round   2 of   2, 101 of 1064 nodes\n+     31.44 seconds: SPR round   2 of   2, 201 of 1064 nodes\n+     33.04 seconds: SPR round   2 of   2, 301 of 1064 nodes\n+     34.51 seconds: SPR round   2 of   2, 401 of 1064 nodes\n+     36.07 seconds: SPR round   2 of   2, 501 of 1064 nodes\n+     37.52 seconds: SPR round   2 of   2, 601 of 1064 nodes\n+     38.98 seconds: SPR round   2 of   2, 701 of 1064 nodes\n+     40.71 seconds: SPR round   2 of   2, 801 of 1064 nodes\n+     42.29 seconds: SPR round   2 of   2, 901 of 1064 nodes\n+     43.91 seconds: SPR round   2 of   2, 1001 of 1064 nodes\n+     45.04 seconds: ME NNI round 25 of 36, 1 of 531 splits\n+     45.22 seconds: ME NNI round 25 of 36, 201 of 531 splits, 1 c'..b'71.87 seconds: Site likelihoods with rate category 11 of 20\n+     72.25 seconds: Site likelihoods with rate category 12 of 20\n+     72.62 seconds: Site likelihoods with rate category 13 of 20\n+     72.99 seconds: Site likelihoods with rate category 14 of 20\n+     73.36 seconds: Site likelihoods with rate category 15 of 20\n+     73.74 seconds: Site likelihoods with rate category 16 of 20\n+     74.11 seconds: Site likelihoods with rate category 17 of 20\n+     74.49 seconds: Site likelihoods with rate category 18 of 20\n+     74.86 seconds: Site likelihoods with rate category 19 of 20\n+     75.24 seconds: Site likelihoods with rate category 20 of 20\n+Switched to using 20 rate categories (CAT approximation)\n+Rate categories were divided by 0.780 so that average rate = 1.0\n+CAT-based log-likelihoods may not be comparable across runs\n+Use -gamma for approximate but comparable Gamma(20) log-likelihoods\n+     75.44 seconds: ML NNI round 2 of 18, 1 of 531 splits\n+     77.30 seconds: ML NNI round 2 of 18, 101 of 531 splits, 6 changes (max delta 8.408)\n+     79.63 seconds: ML NNI round 2 of 18, 201 of 531 splits, 16 changes (max delta 11.916)\n+     81.66 seconds: ML NNI round 2 of 18, 301 of 531 splits, 26 changes (max delta 12.582)\n+     83.77 seconds: ML NNI round 2 of 18, 401 of 531 splits, 37 changes (max delta 12.582)\n+     85.45 seconds: ML NNI round 2 of 18, 501 of 531 splits, 45 changes (max delta 12.582)\n+ML-NNI round 2: LogLk = -243521.538 NNIs 47 max delta 12.58 Time 86.22\n+     86.22 seconds: ML NNI round 3 of 18, 1 of 531 splits\n+     87.60 seconds: ML NNI round 3 of 18, 101 of 531 splits, 2 changes (max delta 2.600)\n+     89.51 seconds: ML NNI round 3 of 18, 201 of 531 splits, 10 changes (max delta 3.628)\n+     90.90 seconds: ML NNI round 3 of 18, 301 of 531 splits, 12 changes (max delta 3.628)\n+ML-NNI round 3: LogLk = -243454.047 NNIs 17 max delta 4.33 Time 92.41\n+     92.40 seconds: ML NNI round 4 of 18, 1 of 531 splits\n+     93.59 seconds: ML NNI round 4 of 18, 101 of 531 splits, 0 changes\n+     94.89 seconds: ML NNI round 4 of 18, 201 of 531 splits, 4 changes (max delta 8.267)\n+ML-NNI round 4: LogLk = -243401.668 NNIs 8 max delta 15.05 Time 95.80\n+     95.79 seconds: ML NNI round 5 of 18, 1 of 531 splits\n+     97.12 seconds: ML NNI round 5 of 18, 101 of 531 splits, 1 changes (max delta 5.470)\n+ML-NNI round 5: LogLk = -243385.290 NNIs 5 max delta 5.47 Time 97.70\n+     97.69 seconds: ML NNI round 6 of 18, 1 of 531 splits\n+ML-NNI round 6: LogLk = -243379.465 NNIs 0 max delta 0.00 Time 98.56\n+Turning off heuristics for final round of ML NNIs (converged)\n+     98.55 seconds: ML NNI round 7 of 18, 1 of 531 splits\n+    101.64 seconds: ML NNI round 7 of 18, 101 of 531 splits, 3 changes (max delta 5.543)\n+    104.85 seconds: ML NNI round 7 of 18, 201 of 531 splits, 4 changes (max delta 5.543)\n+    107.89 seconds: ML NNI round 7 of 18, 301 of 531 splits, 8 changes (max delta 5.543)\n+    111.07 seconds: ML NNI round 7 of 18, 401 of 531 splits, 9 changes (max delta 5.543)\n+    114.20 seconds: ML NNI round 7 of 18, 501 of 531 splits, 12 changes (max delta 20.657)\n+ML-NNI round 7: LogLk = -243045.843 NNIs 13 max delta 20.66 Time 115.43 (final)\n+    115.43 seconds: ML Lengths 1 of 531 splits\n+    116.25 seconds: ML Lengths 101 of 531 splits\n+    117.06 seconds: ML Lengths 201 of 531 splits\n+    117.84 seconds: ML Lengths 301 of 531 splits\n+    118.68 seconds: ML Lengths 401 of 531 splits\n+    119.49 seconds: ML Lengths 501 of 531 splits\n+Optimize all lengths: LogLk = -243039.348 Time 120.01\n+    129.12 seconds: ML split tests for    100 of    530 internal splits\n+    138.49 seconds: ML split tests for    200 of    530 internal splits\n+    148.16 seconds: ML split tests for    300 of    530 internal splits\n+    156.37 seconds: ML split tests for    400 of    530 internal splits\n+    165.18 seconds: ML split tests for    500 of    530 internal splits\n+Total time: 167.98 seconds Unique: 533/533 Bad splits: 5/530 Worst delta-LogLk 10.254\n'
b
diff -r 000000000000 -r b2b9795cc862 fasttree/test-data/tree.nhx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/test-data/tree.nhx Thu May 29 23:53:21 2014 -0400
b
b'@@ -0,0 +1,1 @@\n+(((323827;size=1;:0.02068,356135;size=1;:0.01598)1.000:0.16731,((144091;size=1;:0.00935,74326;size=1;:0.02447)1.000:0.11302,(((268641;size=1;:0.05720,266385;size=1;:0.07226)1.000:0.11638,(24341;size=1;:0.04904,40042;size=1;:0.07996)1.000:0.14106)0.922:0.01593,((((119942;size=1;:0.01062,316958;size=1;:0.01805)1.000:0.05804,((326871;size=1;:0.02587,(111504;size=1;:0.01783,335588;size=1;:0.01246)0.892:0.00441)1.000:0.08828,(176763;size=1;:0.00892,(234581;size=1;:0.02244,337963;size=1;:0.01425)0.959:0.00933)1.000:0.05516)0.917:0.01880)1.000:0.05482,(230312;size=1;:0.13145,((((161217;size=1;:0.06466,134657;size=1;:0.03829)1.000:0.03320,(250261;size=1;:0.06341,(346553;size=1;:0.02047,256408;size=1;:0.01631)1.000:0.04352)0.958:0.01645)0.999:0.02607,254951;size=1;:0.08589)0.942:0.01664,(339114;size=1;:0.07228,355710;size=1;:0.10976)0.968:0.02747)0.721:0.00915)0.998:0.03922)1.000:0.04837,(((223034;size=1;:0.19172,(202396;size=1;:0.13594,(331359;size=1;:0.11249,((305476;size=1;:0.03714,339941;size=1;:0.06705)1.000:0.05306,(345452;size=1;:0.12376,((355928;size=1;:0.04645,321569;size=1;:0.03957)1.000:0.05018,(330590;size=1;:0.07117,343697;size=1;:0.05937)0.941:0.02319)0.992:0.03125)0.466:0.01984)0.146:0.02341)1.000:0.14853)0.028:0.05421)1.000:0.42189,(230061;size=1;:0.20730,(158129;size=1;:0.12692,(200586;size=1;:0.08111,(252268;size=1;:0.03165,(335331;size=1;:0.01391,50882;size=1;:0.06307)0.984:0.03944)0.411:0.01718)0.992:0.05070)0.994:0.05330)0.906:0.04192)0.974:0.04470,((((251541;size=1;:0.14578,156037;size=1;:0.14492)0.971:0.05385,((201276;size=1;:0.15208,(135161;size=1;:0.14829,222960;size=1;:0.12396)0.992:0.04992)0.969:0.02894,(216910;size=1;:0.18342,(242956;size=1;:0.19528,((213358;size=1;:0.12362,328135;size=1;:0.11415)1.000:0.09750,((200083;size=1;:0.09767,(105625;size=1;:0.08556,((224964;size=1;:0.07442,203214;size=1;:0.08154)1.000:0.03881,(277716;size=1;:0.09582,(201338;size=1;:0.04064,(215422;size=1;:0.09287,210146;size=1;:0.04623)0.985:0.02111)0.961:0.01916)0.970:0.01508)0.964:0.01597)0.904:0.01826)0.957:0.02687,((104633;size=1;:0.09222,(192224;size=1;:0.03964,(248390;size=1;:0.03617,(328891;size=1;:0.03297,10978;size=1;:0.02760)0.703:0.01429)0.970:0.01682)1.000:0.06372)0.990:0.03158,(278064;size=1;:0.09169,110455;size=1;:0.11506)0.708:0.02929)0.835:0.01832)1.000:0.05950)0.618:0.02257)0.970:0.03033)0.884:0.01713)0.947:0.02838)0.966:0.03109,((203534;size=1;:0.05889,287458;size=1;:0.06672)1.000:0.25499,((103462;size=1;:0.11834,(272920;size=1;:0.07621,270990;size=1;:0.04117)1.000:0.07441)0.999:0.05961,(202507;size=1;:0.19712,200237;size=1;:0.25432)0.289:0.02440)1.000:0.08363)0.453:0.03305)0.899:0.02749,((194242;size=1;:0.06507,(89159;size=1;:0.06746,(333899;size=1;:0.03790,(111978;size=1;:0.02136,344719;size=1;:0.02477)0.970:0.01613)0.907:0.02062)1.000:0.05254)1.000:0.10306,(318624;size=1;:0.15031,230687;size=1;:0.20654)0.995:0.05244)0.917:0.02003)0.946:0.03531)0.448:0.01640)0.888:0.01582)0.914:0.01992)0.000:0.00697)0.712:0.01331,(((311045;size=1;:0.15922,((((329997;size=1;:0.00988,(257979;size=1;:0.01825,122043;size=1;:0.01605)0.702:0.00633)1.000:0.06426,(333779;size=1;:0.11933,(107214;size=1;:0.01042,342352;size=1;:0.06049)0.998:0.03656)0.997:0.04098)0.443:0.00807,(183636;size=1;:0.06746,(237311;size=1;:0.05672,(((352989;size=1;:0.03114,356234;size=1;:0.01204)0.985:0.01357,(354604;size=1;:0.02721,325262;size=1;:0.02020)0.930:0.00582)0.992:0.02396,(138400;size=1;:0.05539,(306861;size=1;:0.09095,(6887;size=1;:0.03999,((((((349195;size=1;:0.01411,328876;size=1;:0.01328)0.504:0.00392,(154953;size=1;:0.01688,155581;size=1;:0.02080)0.911:0.00736)0.996:0.01508,254572;size=1;:0.02771)0.153:0.00286,(342161;size=1;:0.02630,156873;size=1;:0.01797)0.997:0.02081)1.000:0.02282,319461;size=1;:0.03583)0.984:0.01751,(168927;size=1;:0.01484,259583;size=1;:0.04201)0.945:0.00963)0.781:0.01330)0.343:0.00829)0.991:0.01948)0.995:0.02129)0.995:0.02074)1.000:0.04294)0.974:0.01795)0.905:0.01779,(((173267;size=1;:0.04139,172219;size=1;'..b'0.01765)0.990:0.01342,(((100077;size=1;:0.01641,(323976;size=1;:0.03050,278158;size=1;:0.02433)0.992:0.01565)0.983:0.01976,(153421;size=1;:0.05862,254573;size=1;:0.07677)0.845:0.01601)0.964:0.01538,(((334050;size=1;:0.02454,246595;size=1;:0.03873)1.000:0.04852,(231092;size=1;:0.04058,272292;size=1;:0.03184)0.581:0.00765)0.987:0.01478,((156530;size=1;:0.01809,(173254;size=1;:0.01733,231876;size=1;:0.02135)0.984:0.01431)1.000:0.03215,269565;size=1;:0.04423)0.339:0.00904)0.785:0.00817)0.936:0.00789)0.982:0.00837)0.846:0.00469)0.596:0.00578,((((103229;size=1;:0.03477,102526;size=1;:0.04775)0.986:0.01651,(249254;size=1;:0.01431,308722;size=1;:0.01055)0.864:0.01184)0.925:0.01365,326618;size=1;:0.02183)1.000:0.04019,136955;size=1;:0.09462)0.651:0.01389)0.986:0.02203)0.043:0.00825,(275936;size=1;:0.07621,194302;size=1;:0.04459)0.998:0.03498)0.940:0.01577)0.000:0.01453)0.671:0.01475)0.998:0.03322)1.000:0.03603)0.504:0.01478)0.969:0.02460)0.989:0.03428,((137211;size=1;:0.08432,159771;size=1;:0.05238)1.000:0.05282,(108876;size=1;:0.06944,((138691;size=1;:0.02874,(228291;size=1;:0.00567,(68979;size=1;:0.01542,107060;size=1;:0.01911)0.994:0.01092)0.979:0.01108)0.996:0.01575,((232479;size=1;:0.01394,337085;size=1;:0.03588)1.000:0.01884,354066;size=1;:0.09344)0.678:0.00789)0.981:0.01655)0.906:0.01894)1.000:0.07047)0.982:0.03022)0.927:0.01186,((((((((((270810;size=1;:0.01712,310703;size=1;:0.02311)1.000:0.02360,(343596;size=1;:0.01623,(350342;size=1;:0.02578,354780;size=1;:0.03339)0.245:0.00731)0.569:0.00658)0.963:0.00901,(152391;size=1;:0.04500,(348982;size=1;:0.03616,351014;size=1;:0.03211)0.981:0.01306)0.854:0.00882)0.697:0.01047,303962;size=1;:0.04018)0.858:0.00754,336157;size=1;:0.04980)1.000:0.04124,((229972;size=1;:0.02913,161055;size=1;:0.02907)0.840:0.00921,(354222;size=1;:0.04343,(346047;size=1;:0.00981,313417;size=1;:0.02681)1.000:0.02603)0.971:0.01454)0.915:0.01470)0.994:0.02139,((231803;size=1;:0.15941,(356095;size=1;:0.00243,(116062;size=1;:0.02018,334058;size=1;:0.02340)0.952:0.01197)1.000:0.08263)1.000:0.06469,(((12727;size=1;:0.05817,366993;size=1;:0.10403)0.993:0.02092,((11816;size=1;:0.04969,(58304;size=1;:0.09000,(146560;size=1;:0.03179,((12295;size=1;:0.02322,(90191;size=1;:0.01875,(269511;size=1;:0.02576,(259900;size=1;:0.01001,(161643;size=1;:0.02098,(343226;size=1;:0.01226,311857;size=1;:0.01564)0.991:0.01306)0.783:0.00793)0.696:0.01007)0.055:0.00645)0.769:0.00435)0.263:0.00479,(99149;size=1;:0.01224,(140315;size=1;:0.01884,(370143;size=1;:0.01104,(21520;size=1;:0.01944,12214;size=1;:0.01742)1.000:0.02571)0.000:0.00547)0.507:0.00669)0.937:0.00889)1.000:0.02973)0.727:0.01128)0.775:0.00458)0.987:0.01203,(285203;size=1;:0.07039,((236904;size=1;:0.03822,241868;size=1;:0.01876)0.990:0.01598,(46572;size=1;:0.02620,((250779;size=1;:0.07198,(115193;size=1;:0.02361,197531;size=1;:0.03525)0.919:0.01053)0.982:0.01347,154823;size=1;:0.02474)0.971:0.01113)0.974:0.01196)0.803:0.00504)0.960:0.01052)0.652:0.00446)0.990:0.01476,((114582;size=1;:0.03729,(((343734;size=1;:0.01935,(306632;size=1;:0.06398,((((312194;size=1;:0.02026,307760;size=1;:0.01325)0.995:0.01290,(237234;size=1;:0.01455,339527;size=1;:0.01301)0.960:0.00924)0.206:0.00443,(258157;size=3;:0.01122,(334255;size=1;:0.01607,247612;size=1;:0.00671)0.980:0.00685)1.000:0.02074)0.615:0.00742,264759;size=1;:0.01422)0.791:0.01131)1.000:0.02246)0.999:0.02034,267662;size=1;:0.03743)0.945:0.00819,((340660;size=3;:0.02154,346841;size=1;:0.02043)1.000:0.03953,152577;size=1;:0.04447)0.981:0.01294)0.603:0.00492)0.684:0.01084,252888;size=1;:0.02916)0.786:0.00982)1.000:0.04139)0.599:0.00969)0.998:0.03032,((58121;size=1;:0.02423,327693;size=1;:0.06436)0.994:0.03321,(354595;size=1;:0.07961,348274;size=1;:0.03945)0.805:0.01539)0.999:0.03594)0.990:0.02551,(101310;size=1;:0.04572,242567;size=1;:0.06918)1.000:0.13493)0.934:0.01492,((332023;size=1;:0.01421,324366;size=1;:0.05922)1.000:0.13415,(62482;size=1;:0.05687,261860;size=1;:0.03283)1.000:0.18043)0.841:0.01470)0.959:0.01761)0.153:0.00823);\n'
b
diff -r 000000000000 -r b2b9795cc862 fasttree/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasttree/tool_dependencies.xml Thu May 29 23:53:21 2014 -0400
b
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="FastTree" version="2.17">
+        <install version="1.0">
+           <actions_group>
+           <!-- Download the executable for 64-bit OSX. -->
+             <actions os="linux" architecture="x86_64">
+                <action type="download_by_url">http://www.microbesonline.org/fasttree/FastTree</action>
+ <action type="move_file">
+                    <source>FastTree</source>
+                    <destination>$INSTALL_DIR/fasttree</destination>
+                </action>
+ <action type="shell_command">chmod ugo+x $INSTALL_DIR/fasttree/FastTree</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/fasttree</environment_variable>
+                </action>
+              </actions>
+              <!-- This actions tag is only processed if tried to install on a none-linux-64-bit system. -->
+              <actions>
+                <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported. This version of FastTree is just intended for Linux 64-bit systems.</action>
+              </actions>
+            </actions_group>
+        </install>
+    </package>
+</tool_dependency>