PB Generate tree - mendessoares/BuddySuite GitHub Wiki

--generate_tree, -gt

Description

Unlike the other tools in PhyloBuddy, 'generate_tree' takes an alignment as input and requires that AlignBuddy is installed on your system. AlignBuddy and PhyloBuddy will do the necessary preprocessing of your alignment so it can be used by the inference software selected. Any new trees generated will be output in Newick format by default, but the -o flag can be used to override this behavior.

Most inference tools write temporary and support files, all of which are discarded by generate_tree once the run is complete unless you specifically choose to save them with the -k flag.

Inference tools currently supported

Note that these programs are not bundled with BuddySuite, so you are responsible for getting them correctly installed and into your $PATH. Older versions of the tools may work but are currently untested.

• RAxML V.8+
• PHYML 20120412
• FastTree V.2+

Arguments

Inference tool ( {raxml | phyml | fasttree} )

Optional. The program PhyloBuddy uses to generate your new tree(s). Note that the program name must be exactly as written above (make a symbolic link if necessary). If no value is provided, then generate_tree will search your system for each in order, creating a tree with the first program found.

Program specific parameters ( str )

Optional. There are many optional parameters that each of these inference tools may accept (see their documentation for details). PhyloBuddy will provide the necessary number of default arguments to ensure the program runs (e.g., evolutionary model), but these may not be the most appropriate for your data set and should only be used for 'quick-and-dirty' analyses.

Examples

Input file: Mnemiopsis.nex

#NEXUS
begin data;
	dimensions ntax=5 nchar=333;
	format datatype=dna missing=? gap=-;
matrix
'Mle-Panxα6'  ---atgttattggagatattagc---gaacttcaaaggagcgacacctttcaaagaaatagttctagatgacaagtgggaccagattaaccgatgttacatgttcctgctgtgtgtgattttcggaactgtcgtgacattcagacagtataccgg--tggtatcattgcttgtgacggtctgacaaagt----------------------tctcagctgcctttgcggaggactattgctggacgcagggtctttataccataaaggaggcgtatgacatagtggataattccttaccttacccaggactgctaccggaagatgcgcct---
'Mle-Panxα9'  ------atgttagacatactttc---aaagtttaaaggagttactccttttaaaggtataacgatagatgacgggtgggatcaactcaatcggagttttatgttcgtcctgctcgttgtcatgggaacgactgtcactgtccggcaatacaccgg--cagtgtcatcagttgtgacggcttcaaaaagt----------------------ttggatccacttttgcggaggattactgttggacccagggactgtacacagttttagaaggatatgaccaacccagccaaaatatcccttacccaggcctccttccagacgaggcaccaccc
'Mle-Panxα11' atgctgatctcgagcttagttc------agttcagcaggttatctccttttaaggagataactatagatgacgggtgggaccaacttaacaggagtttcatgttcgttctgatggttatctgtggaactatcgtcactgtccgacaacatacagg--taacatcatctcgtgtaacggtttcacaaaat----------------------acgacggatccttctccgaggactactgctggacgcagggactctacacgatcagggaggcgtaccacgtgagcgacgtcaacgtcccttatcccggagttatcccggaggagatccca---
'Mle-Panxα3'  atgttgttgctcggctcactcgg---aacgatcaagaacttgagcatcttcaaagacctgtccttggacgactggctggatcagatgaacaggaccttcatgtttctactgctctgtttcatgggaacaattgtcgccgttagtcagtacactgg--taaaaacatatcttgcgatggctttacgaagt----------------------tcggagaagatttctcgcaagactactgctggacccagggcttgtacacgattaaagaagcgtacgacttgcccgagtcccagatcccgtatcctgggattatccctgaaaacgtg------
'Mle-Panxα2'  ---atggtattggatctcatttctggaagcttgaatggctttttaaagatcaagtcagttagcatcgacgatcagtgggaccagattaacagaacctatttggtcatgttttgtattttatctggtacaatcatgacctttaaacagaatttaggatcaataatacactgtatatcggatgcaagaggcgacgacagttcgtttgcggatgctcatgcgacatttgtgcaagactattgtgctgctcaagggctgtacactttaaaagaagtgtatgacaag---------------tcttggccagatgaaattcct---------------
;
end;

Usage example 1

$: pb Mnemiopsis.nex -gt

Output

(('Mle-Panxα9':0.3059348496381305,('Mle-Panxα11':0.2598946477760956,'Mle-Panxα3':0.5755107707842939):0.09758742685282855):0.25355092098261167,'Mle-Panxα2':1.2066740495820707,'Mle-Panxα6':0.19944740625275767):0.0;

Usage example 2

$: pb Mnemiopsis.nex -gt phyml -o nexus

Output

#NEXUS

BEGIN TAXA;
    DIMENSIONS NTAX=5;
    TAXLABELS
        'Mle-Panxα6'
        'Mle-Panxα2'
        'Mle-Panxα9'
        'Mle-Panxα11'
        'Mle-Panxα3'
  ;
END;

BEGIN TREES;
    TREE 1 = ('Mle-Panxα6':0.18789485,'Mle-Panxα2':1.19857441,('Mle-Panxα9':0.31054892,('Mle-Panxα11':0.26525421,'Mle-Panxα3':0.59025685)0.648000:0.08613268)0.841000:0.2564462);
END;

Usage example 3

$: pb Mnemiopsis.nex -gt raxml '-m GTRCAT -p 112358'

Output

(('Mle-Panxα9':0.3210138351992049,('Mle-Panxα3':0.606902403021969,'Mle-Panxα11':0.2665054046846879):0.10307555147917344):0.2745329411057646,'Mle-Panxα2':1.2930048140099493,'Mle-Panxα6':0.1975572026655663):0.0;