RSS Feed ComAlign
ComAlign extracts qualitatively good sub alignments from a set of multiple alignments and combines them in a new, often improved alignment.
Installed on the: opteron cluster.
Usage on bioinformatics and codon
Executables are:
- /biomed/src/comalign/generate/DNAgen
/biomed/src/comalign/combine/ComAlign
/biomed/src/comalign/profile/ProfAlign
DNAgen is used to generate sequences in the Gen-Al format.
/biomed/src/comalign/generate/DNAgen -arguments
where the arguments can be:
| -h| H | help |
| -s | random seed number |
| -n | number of sequences to generate |
| -l | initial length of 'eve' |
| -m | max. length of sequences |
| -g | number of generations to simulate |
ComAlign, given a number of sequences, generates heuristic alignments combined in the best way possible.
/biomed/src/comalign/combine/ComAlign -arguments
where the arguments can be: (defaults shown in parentheses)
| -h| H | Help |
| -s | 'random seed' number (1) |
| -n | Number of sequences that are to be aligned (2) |
| -i | Number of iterations in ComAlign [on each iteration a new alignment is added to the pool of alignments ComAlign is working on] (10) |
| -l | ComAlign records the time it took to find a solution as good as the score denoted by l |
| -t | ComAlign marks the best solution found after t 1/100 seconds |
| -c | Makes ComAlign terminate if the score hasn't changed within the last c iterations (20) |
| -a | On termination ComAlign will print the best found alignment |
| -f | name of input file (stdin) |
ProfALign
/biomed/src/comalign/profile/ProfAlign -arguments
where the arguments can be:
| -h| H | Help |
| -s | random seed number |
| -n | number of sequences to align |
Documentation
See instructions on using ComAlign.
See also
- Other sequence analysis software installed at PSC.