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.TH "alignment-distances" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment-distances\f[R] - Compute distances between alignments.
.SH SYNOPSIS
.PP
\f[B]alignment-distances\f[R] \f[I]analysis\f[R] alignments-file1
[alignments-file2 \&...]
.SH DESCRIPTION
.PP
Compute distances between alignments.
.SH INPUT OPTIONS:
.TP
\f[B]-h\f[R], \f[B]\[en]help\f[R]
Produce help message
.TP
\f[B]-s\f[R] \f[I]arg\f[R] (=0), \f[B]\[en]skip\f[R] \f[I]arg\f[R] (=0)
Number of alignment samples to skip.
.TP
\f[B]-m\f[R] \f[I]arg\f[R] (=1000), \f[B]\[en]max\f[R] \f[I]arg\f[R] (=1000)
Maximum number of alignments to analyze.
.TP
\f[B]-V\f[R], \f[B]\[en]verbose\f[R]
Output more log messages on stderr.
.TP
\f[B]\[en]alphabet\f[R] \f[I]arg\f[R]
Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets,
Codons, or Codons+stop.
.SH ANALYSIS OPTIONS:
.TP
\f[B]\[en]distances\f[R] \f[I]arg\f[R]
(=splits:splits2:nonrecall:inaccuracy) Colon-separated list of
distances.
.TP
\f[B]\[en]analysis\f[R] \f[I]arg\f[R]
Analysis: score, AxA, NxN, compare, median, distances
.TP
\f[B]\[en]CI\f[R] \f[I]arg\f[R] (=0.94999999999999996)
Confidence interval size.
.TP
\f[B]\[en]mean\f[R]
Show mean and standard deviation
.TP
\f[B]\[en]median\f[R]
Show median and confidence interval
.TP
\f[B]\[en]minmax\f[R]
Show minimum and maximum distances
.SH EXAMPLES:
.PP
Compute distances from true.fasta to each in As.fasta:
.IP
.nf
\f[C]
% alignment-distances score true.fasta As.fasta
\f[R]
.fi
.PP
Compute distance matrix between all pairs of alignments in all files:
.IP
.nf
\f[C]
% alignment-distances AxA file1.fasta ... fileN.fasta
\f[R]
.fi
.PP
Compute all NxN pairwise alignment accuracies, averaged over As:
.IP
.nf
\f[C]
% alignment-distances NxN true.fasta As.fasta
\f[R]
.fi
.PP
Find alignment with smallest average distance to other alignments:
.IP
.nf
\f[C]
% alignment-distances median As.fasta A.fasta
\f[R]
.fi
.PP
Compare the distances with-in and between the two groups:
.IP
.nf
\f[C]
% alignment-distances compare A-dist1.fasta A-dist2.fasta
\f[R]
.fi
.PP
Report distribution of average distance to other alignments:
.IP
.nf
\f[C]
% alignment-distances distances As.fasta A.fasta
\f[R]
.fi
.SH REPORTING BUGS:
.PP
BAli-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.