NAME

alignment-distances - Compute distances between alignments.

SYNOPSIS

alignment-distances analysis alignments-file1 [alignments-file2 ...]

DESCRIPTION

Compute distances between alignments.

INPUT OPTIONS:

-h, --help

Produce help message

-s arg (=0), --skip arg (=0)

Number of alignment samples to skip.

-m arg (=1000), --max arg (=1000)

Maximum number of alignments to analyze.

-v, --verbose

Output more log messages on stderr.

--alphabet arg

Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.

ANALYSIS OPTIONS:

--distances arg

(=splits:splits2:nonrecall:inaccuracy) Colon-separated list of distances.

--analysis arg

Analysis: score, AxA, NxN, compare, median, distances

--CI arg (=0.94999999999999996)

Confidence interval size.

--mean

Show mean and standard deviation

--median

Show median and confidence interval

--minmax

Show minimum and maximum distances

EXAMPLES:

Compute distances from true.fasta to each in As.fasta:

% alignment-distances score true.fasta As.fasta

Compute distance matrix between all pairs of alignments in all files:

% alignment-distances AxA file1.fasta ... fileN.fasta

Compute all NxN pairwise alignment accuracies, averaged over As:

% alignment-distances NxN true.fasta As.fasta

Find alignment with smallest average distance to other alignments:

% alignment-distances median As.fasta A.fasta

Compare the distances with-in and between the two groups:

% alignment-distances compare A-dist1.fasta A-dist2.fasta

Report distribution of average distance to other alignments:

% alignment-distances distances As.fasta A.fasta

REPORTING BUGS:

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

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