1430 days ago
Set up WGD environment using conda !
...Usage: wgd [OPTIONS] COMMAND [ARGS]... Welcome to the wgd command line interface!...distributions. pre Check and optionally rename CDS files. syn Co-linearity analyses. viz Plot h...1231 days ago
Perl script to run awk inside perl
.../perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indigestible) eva...1191 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1024 days ago
1018 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 scheme my $MAT...978 days ago
978 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is available in the legacy NCBI BLAST...978 days ago
Inreractive SCP / File transfer !
.../ Directory using scp" #next line check if entered value is not...x$desthost = "x" ]; do #next line prints what userd should ente...ishes while loop done #next line check if entered value is not...$filename" = "x" ]; do #next line prints what userd should ente...978 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ h...971 days ago