NAME
alignment-find - Find conserved parts of an
alignment.
SYNOPSIS
alignment-find conserved alignment-file
[OPTIONS]
DESCRIPTION
Find conserved parts of an alignment.
ALLOWED OPTIONS:
- -h, --help
-
produce help message
- --align arg (=-)
-
file with alignment to convert (default STDIN)
- --tree arg
-
file with initial tree
- --alphabet arg
-
specify the alphabet: DNA, RNA, Amino-Acids, Triplets, or Codons
- --groups arg
-
file with taxon groups
- --split arg
-
a split to consider
- --ignore-rate-change
-
ignore rate changes
- --require-conservation
-
Highlight conserved regions
- --require-change
-
Highlight regions if conservation changes
- --require-all-different
-
Taxa differences are interesting of there is no letter overlap
REPORTING BUGS:
BAli-Phy online help: http://www.bali-phy.org/docs.php.
Please send bug reports to bali-phy-users@googlegroups.com.