NAME
alignment-consensus - Construct a consensus alignment to summarize an alignment sample.
SYNOPSIS
alignment-consensus alignments-file [alignments-file ...] [OPTIONS]
DESCRIPTION
Construct a consensus alignment to summarize an alignment sample.
ALLOWED OPTIONS:
- -h, –help
-
produce help message
- –alphabet arg
-
Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.
- -s arg (=0), –skip arg (=0)
-
number of alignment samples to skip
- -m arg (=1000), –max arg (=1000)
-
maximum number of alignments to analyze
- –strict arg
-
ignore events below this probability
- –cutoff arg
-
ignore events below this probability
- –uncertainty arg
-
file-name for AU uncertainty vs level
- –chop-to arg
-
keep only the first arg taxa
- -V, –verbose
-
Output more log messages on stderr.
REPORTING BUGS:
BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.