FastME 2.0

Input files

Phylip file:

4   120
Orangutan   CCAAACGACA TTTCATATGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTGTCCGGAA
Gorilla     CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA
Human       CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATAAGA GACAAGTGAG CTCTCCGAAA
Chimp       CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA

            CCAACATATC AGACATATGT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
            CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
            CCAAGATACC AGACATTTGT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT
            CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT

Parameters

Output name: Newick tree
Evolutionary model : TN93
Distance method : BIONJ

Output file

Newick tree:

((Gorilla:0.005755,Orangutan:0.020680):0.001063,Human:0.006655,Chimp:0.002132);

OPTIONS

-i file, --input_data=file
	The input data file contains sequence alignment(s) or a distance matrix(ces).
-u input_tree_file, --user_tree=input_tree_file
	FastME may use an existing topology available in the input user tree file which corresponds to the input dataset.
-o output_tree_file, --output_tree=output_tree_file
	FastME will write the infered tree into the output tree file.
-O output_matrix_file, --output_matrix=output_matrix_file
	Use output matrix file option if you want FastME to write the distances matrix computed from the input alignment in the output matrix file.
-I output_information_file, --output_info=output_information_file
	Use this option if you want FastME to write information about its execution in the output information file.
-B output_bootstrap_trees_file, --output_boot=output_bootstrap_trees_file
	Use this option if you want FastME to write bootstrap trees in the bootstrap trees file.
-a, --append	Use this option to append results to existing output files (if any). By default output files will be overwritten.
-m method, --method=method
	FastME computes a tree using a distance algorithm. You may choose this method from: TaxAdd_(B)alME, TaxAdd_(O)LSME, B(I)ONJ (default), (N)J or (U)NJ.
-d model, --dna=model
	Use this option if your input data file contains DNA sequences alignment(s). You may also indicate the evolutionary [model] which can be choosen from: (p)-distance, R(Y) symmetric, (R)Y, (J)C69, (K)2P, F8(1), F8(4) (default), (T)N93, (L)ogDet.
-p model, --protein=model
	Use this option if your input data file contains protein sequences alignment(s). You may also indicate the evolutionary [model] which can be choosen from: (p)-distance, (F)81 like, (L)G (default), (W)AG, (J)TT, Day(h)off, (D)CMut, (C)pRev, (M)tREV, (R)tREV, HIV(b), H(I)Vw or FL(U).
-r, --remove_gap
	Use this option to completely remove any site which has a gap in any sequence. By default, FastME is doing pairwise deletion of gaps.
-e, --equilibrium
	The equilibrium frequencies for DNA are always estimated by counting the occurence of the nucleotides in the input alignment. For amino-acid sequences, the equilibrium frequencies are estimated using the frequencies defined by the substitution model. Use this option if you whish to estimate the amino-acid frequencies by counting their occurence in the input alignment.
-g alpha, --gamma=alpha
	Use this option if you wish to have gamma distributed rates across sites. By default, FastME runs with no gamma variation. If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0. Only helpful when the input data file contains sequences alignment(s).
-n NNI, --nni=NNI
	Use this option to do [NNI] tree topology improvement. You may choose the [NNI] type from: NNI_(B)alME (default) or NNI_(O)LS.
-s, --spr	Use this option to do SPR tree topology improvement.
-w branch, --branch_length=branch
	Use this option to indicate the branch length to assign to the tree. Only helpful when not improving the tree topology (no NNI nor SPR). You may choose the branch length from: (B)alLS (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.
-D datasets, --datasets=datasets
	Use this option to indicate the number of datasets in your input data file. Default value is 1.
-b replicates, --bootstrap=replicates
	Use this option to indicate the number of replicates FastME will do for bootstrapping. Default value is 0. Only helpful when the input data file contains sequences alignment(s).
-z seed, --seed=seed
	Use this option to initialize randomization with seed value. Only helpful when bootstrapping.
-c	Use this option if you want FastME only to compute distance matrix. Only helpful when the input data file contains sequences alignment(s).
-T number_of_threads, --nb_threads=number_of_threads
	Use this option to set the number of threads to use. Default number of threads is 4.
-v value, --verbose=value
	Sets the verbose level to value [0-3]. Default value is 0
-V, --version	Prints the FastME version.
-h, --help	Display this usage.