.\" Automatically generated by Pandoc 2.2.1
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.TH "alignment\-distances" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]alignment\-distances\f[] \- Compute distances between alignments.
.SH SYNOPSIS
.PP
\f[B]alignment\-distances\f[] \f[I]analysis\f[] alignments\-file1
[alignments\-file2 ...]
.SH DESCRIPTION
.PP
Compute distances between alignments.
.SH INPUT OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
Produce help message
.RS
.RE
.TP
.B \f[B]\-s\f[] \f[I]arg\f[] (=0), \f[B]\-\-skip\f[] \f[I]arg\f[] (=0)
Number of alignment samples to skip.
.RS
.RE
.TP
.B \f[B]\-m\f[] \f[I]arg\f[] (=1000), \f[B]\-\-max\f[] \f[I]arg\f[] (=1000)
Maximum number of alignments to analyze.
.RS
.RE
.TP
.B \f[B]\-v\f[], \f[B]\-\-verbose\f[]
Output more log messages on stderr.
.RS
.RE
.TP
.B \f[B]\-\-alphabet\f[] \f[I]arg\f[]
Specify the alphabet: DNA, RNA, Amino\-Acids, Amino\-Acids+stop,
Triplets, Codons, or Codons+stop.
.RS
.RE
.SH ANALYSIS OPTIONS:
.TP
.B \f[B]\-\-distances\f[] \f[I]arg\f[]
(=splits:splits2:nonrecall:inaccuracy) Colon\-separated list of
distances.
.RS
.RE
.TP
.B \f[B]\-\-analysis\f[] \f[I]arg\f[]
Analysis: score, AxA, NxN, compare, median, distances
.RS
.RE
.TP
.B \f[B]\-\-CI\f[] \f[I]arg\f[] (=0.94999999999999996)
Confidence interval size.
.RS
.RE
.TP
.B \f[B]\-\-mean\f[]
Show mean and standard deviation
.RS
.RE
.TP
.B \f[B]\-\-median\f[]
Show median and confidence interval
.RS
.RE
.TP
.B \f[B]\-\-minmax\f[]
Show minimum and maximum distances
.RS
.RE
.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[]
.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[]
.fi
.PP
Compute all NxN pairwise alignment accuracies, averaged over As:
.IP
.nf
\f[C]
%\ alignment\-distances\ NxN\ true.fasta\ As.fasta
\f[]
.fi
.PP
Find alignment with smallest average distance to other alignments:
.IP
.nf
\f[C]
%\ alignment\-distances\ median\ As.fasta\ A.fasta
\f[]
.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[]
.fi
.PP
Report distribution of average distance to other alignments:
.IP
.nf
\f[C]
%\ alignment\-distances\ distances\ As.fasta\ A.fasta
\f[]
.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.