phyutility (1)

phyutility <command> <options>

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

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

Seach NCBI. For options run phyutility -h ncbisearch.

parse

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

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

Stephen A. Smith http://www.blackrim.org [email protected]