| PHYUTILITY(1) | User Commands | 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>.
- 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
| 2.7.3 | Debian |