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                              alignment-distances(1)