Perl script for calculate Levenshtein distance
sub levenshtein_dist { my ($str1, $str2) = @_; my ($len1, $len2) = (length $str1, length $str2); if ($len1 == 0) { return $len2; } if ($len2 == 0) { return $len1; } my %mat; for (my $i = 0; $i2334 days ago
Create genome scaffolding with Perl
...queryFile, "=21 tab-separated values, got %d)", scalar(@fields)), -verbose => 0}); } ## calculate percent identity my $qAliS...2302 days ago
2258 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads....2134 days ago
2069 days ago
1519 days ago
1334 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring sc...944 days ago
Script to rapid genome clustering based on pairwise ANI
...at the cost of sensitivity: blastn -query -db -outfmt '6 std qlen slen' -max_target_seqs 10000 -perc_identity 90 -o -num_threads 32 Next, calculate pairwise ANI by combining loc...629 days ago
Perl script for chi-squared test !
...$row1 += $file1_ob{$di}; $row2 += $file2_ob{$di}; $total += ($file1_ob{$di} + $file2_ob{$di}); } # now calculate expected values foreach my $di (@dinucs){ # calculate (column total * row total) /...405 days ago