alignment-distances1
Compute distances between alignments.
Usage
alignment-distances analysis
alignments-file1
[alignments-file2 ...]
Overview
Compute distances between alignments.
Input options:
-h,–help-
Produce help message
-sarg (=0),–skiparg (=0)-
Number of alignment samples to skip.
-marg (=1000),–maxarg (=1000)-
Maximum number of alignments to analyze.
-V,–verbose-
Output more log messages on stderr.
–alphabetarg-
Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.
Analysis options:
|
(=splits:splits2:nonrecall:inaccuracy) Colon-separated list of distances. |
|---|---|
|
Analysis: score, AxA, NxN, compare, median, distances |
–CI arg (=0.94999999999999996)
|
Confidence interval size. |
|
Show mean and standard deviation |
|
Show median and confidence interval |
|
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⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
Releases
4 releases since Debian 10 (Buster); the text changed 2 times.