AswinSSoman

for 4.2.4 or higher,4.2.5,4.2.6,4.3.7，it's works ， this is the way which makes Always in evaluation mode 。

1. open Terminal, go to the dir : cd /Applications/Beyond Compare.app/Contents/MacOS
2. change the name BCompare to BCompare.bak: mv BCompare BCompare.bak
3. touch a file name BCompare , and chmod a+u BCompare : touch BCompare && chmod a+u BCompare
4. open BCompare with text editor, insert the script :

#!/bin/bash
rm "/Users/$(whoami)/Library/Application Support/Beyond Compare/registry.dat"
"`dirname "$0"`"/BCompare.bak $@

AswinSSoman

#!/usr/bin/env perl

=head1 NAME

bam2circos.pl - Convert BAM file to Circos plot

=head1 SYNOPSIS

bam2circos.pl [optional] -b FILE

AswinSSoman

#!/usr/local/bin/perl

# 
# Perl script treefam_genelosses.pl
# Written by Avril Coghlan (alc@sanger.ac.uk).
# 28-Aug-06.  
#
# For the TreeFam project.
#
# This perl script connects to the MYSQL database of

AswinSSoman

# Put all genomes' subset contigs into one map file (combined.cmap below)
# this naively uses results dir for all cmaps
# e.g., results/11029A_initial_genome_check/430_subset_103488556_104544470_final.cmap
# also requires RefAligner in root dir
find ./results/ -name "*_final.cmap" > input

rm -f combined.cmap; rm -f combined.idmap
./RefAligner -merge -if input -o combined
rm -f input

AswinSSoman

You can use IGV to automatically & programmatically load genomic datasets and take snapshots of regions of interest. This is very handy and helps you avoid taking many screenshots manually.

Manual page here:

http://software.broadinstitute.org/software/igv/batch

These commands are also available:

http://software.broadinstitute.org/software/igv/PortCommands

AswinSSoman

Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev

[samtools]

AswinSSoman

#!/bin/env perl

use strict;
use warnings;

use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Scalar qw(wrap_array);
use IO::String;

AswinSSoman

Objective - To analyze how the detection of relaxed selection of CYP8B1 gene by RELAX is affected by the following :

• number of gaps
• length of gaps
• number of species

Steps - MSA's and Tree Building

• 1. Select the order and number of species to be used.

AswinSSoman

- Headers

# This is an <h1> tag         
## This is an <h2> tag        
###### This is an <h6> tag     

- Emphasis

AswinSSoman