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 columns of a gap
-M arg (=0), --mask-gaps arg (=0)
Remove columns within columns of a gap
--variant arg (=1)
Is there a SNP at distance 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.