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alignment-distances(1) alignment-distances(1)

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>.

AUTHORS

Benjamin Redelings.
Feb 2018