PHYUTILITY(1)

NAME
phyutility - tools for manipulating sequences and phylogenies

SYNOPSIS
phyutility <command> <options>

DESCRIPTION
Phyutility is a command line program that performs simple analyses or modifications on both trees and data matrices.

OPTIONS
To get help on a specific command use option -h <command>

  COMMANDS
for trees:

consensus
     Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>.

convert
     Convert tree files. Use like -vert -in <infile> -out <outfile>.

leafstab
     Leaf stability index calculation. Use like -ls -in <infile>.

linmove
     Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>.

prune
     Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>.

reroot
     Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>.

thin
     Thin trees. Use like -tt # -in <infile> -out <outfile>.

treesupp
     Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>.

for seqs:

clean
     Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa <to force aa>.

concat
     Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to force aa>.

ncbiget
     Fetch seqs from NCBI. For options run phyutility -h ncbiget.

ncbisearch
     Search NCBI. For options run phyutility -h ncbisearch.

parse
     Parse genbank results. For options run phyutility -h parse.

EXAMPLE

phyutility -con -t 0.5 -in testall.tre -out test.con
    Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency.

phyutility -vert -in test.tre -out testvert.nex
    Convert the tree file from newick in test.tre into nexus in testvert.nex.

phyutility -concat -in test.aln test2.aln -out testall.nex
    Concatenate 2 alignment files into nexus in testall.nex.

SEE ALSO
See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information.

AUTHOR
Stephen A. Smith http://www.blackrim.org eebsmith@umich.edu