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CANADA: seq_dist

seq_dist (version 1.01)

This program reads DNA sequences from an input file (which contains one sequence in
each line) and compares each pair of consecutive sequences with several distance measures
(so that if n sequences are read n/2 pairs are compared). If you want to measure the
distance between all possible pairs of sequences in a pool, please use seq_dist2. The
results of the comparisons are written to standard output in one table with a line for
each sequence pair and a column for each distance measure.

See the manual for a more detailed description of this tool.
Read the logfile to see what's new in this version.

Download

The program: seq_dist.exe (296 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Example

With input sequences like these:

ttcgccctgctactaacacg
agataacagcaggatttctt
ggatcgcaggatctcagtca
gtgaccctccttccagtccg
gaattccatatcccttccaa
agaccgggctccgcacctgt
cttcacatacaaaattaatc
gtccttcccgcggtttctac

seq_dist produces a table like this:

pair    Hamming(compl.)    HMeasure    HMeasure(compl.)    HDistance    Homology(compl.)    Edit(compl.)
1,2    19    11    13    11    0.45    13
3,4    18    12    12    12    0.4    10
5,6    17    12    13    12    0.4    13
7,8    16    14    14    14    0.3    14
last modification: Jun/20/2008

  
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