Man page - alignment-distances(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

alignment-distances

NAME
SYNOPSIS
DESCRIPTION
INPUT OPTIONS:
ANALYSIS OPTIONS:
EXAMPLES:
REPORTING BUGS:
AUTHORS

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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.

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