Combining many multiple alignments in one improved alignment O. Caprani, K. Bucka-Lassen alignment:multiple comalign comalign perl "ComAlign" 0 seq Sequences File (-f) perl " -f$value" 1 8 seqsfile perl 1 seed Random seed number (-s) perl (defined $value && $value != $vdef) ? " -s$value" : "" 1 1 seqnb Number of sequences that are to be aligned (-n) perl (defined $value && $value != $vdef) ? " -n$value" : "" 2 1 iterations Number of iterations (-i) perl (defined $value && $value != $vdef) ? " -i$value" : "" 10 1 On each iteration a new alignment is added to the pool of alignments ComAlign is working on score score: ComAlign records the time it took to find a solution as good as this score (-l) perl (defined $value) ? " -l$value" : "" 1 time ComAlign marks the best solution found after this number of 1/100 seconds (-t) perl (defined $value) ? " -t$value" : "" 1 last_iterations Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c) perl (defined $value && $value != $vdef) ? " -c$value" : "" 20 1 print_best Print the best found alignment on termination (-a) perl ($value) ? " -a" : "" 1 1