alignment−distances

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 AT googlegroups DOT com>.

AUTHORS

Benjamin Redelings.