NAME

alignment-smc - Generate input for SMC programs.

SYNOPSIS

alignment-smc alignment-file [OPTIONS]

DESCRIPTION

Generate input for SMC programs.

ALLOWED OPTIONS:

-h, --help

produce help message

--align arg

file with sequences and initial alignment

--alphabet arg

specify the alphabet: DNA, RNA, Amino-Acids, Triplets, or Codons

-S, --strip-gaps

Remove columns within arg columns of a gap

-G arg, --mask-gaps arg

Remove columns within arg columns of a gap

-M arg, --mask-file arg

Apply mask-file

--variant arg (=1)

Is there a SNP at distance arg from SNP?

--dical2

Output file for DiCal2

--msmc

Output file for MSMC

--psmc

Output file for PSMC

--autoclean

Mask blocks with too many SNPs

--histogram arg

Output SNP counts for blocks of arg bases

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.