Avril Coghlan avrilcoghlan

Wellcome Trust Sanger Institute
Cambridge, U.K.
http://www.sanger.ac.uk/research/projects/parasitegenomics/

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avrilcoghlan / find_simple_families3.pl

Created March 1, 2013 16:12

Perl script that connects to the TreeFam mysql database, and retrieves all families that have just one human, one rat, one chicken, one Caenorhabditis elegans, and one Drosophila melanogaster gene (as well as possible additional genes from other species).

	#!/usr/local/bin/perl

	#
	# Perl script find_simple_families3.pl
	# Written by Avril Coghlan ([email protected]).
	# 27-Jun-05.
	# Edited 30-Jun-06.
	#
	# For the TreeFam project.
	#

avrilcoghlan / get_orths_from_newick_tree.pl

Created March 1, 2013 16:19

Perl script to read a Newick tree file from TreeFam, and print out the orthologs of a particular input gene based on the tree.

	#!/usr/bin/perl

	#---------------------------------------------------------------------------------------------#
	#
	# A Perl script to read a Newick tree file from Treefam, and
	# print out the orthologues of a particular input gene.
	#
	# Avril Coghlan. 6-Dec-04.
	# [email protected]
	#

avrilcoghlan / map_introns_to_HMM.pl

Created March 1, 2013 16:24

Perl script that reads in an alignment file corresponding to a HMM, and retrieves the positions of introns in the genes from the TreeFam database, and figures out the positions of introns with respect to the HMM columns.

	#!/usr/local/bin/perl

	#
	# Perl script map_introns_to_HMM.pl
	# Written by Avril Coghlan ([email protected])
	# 26-Apr-07.
	#
	# For the TreeFam project.
	#
	# This perl script reads in an alignment file corresponding

avrilcoghlan / parse_treefam_bioperl.pl

Created March 1, 2013 16:26

Perl script that connects to the TreeFam mysql database, and parses the trees using Bioperl.

	#!/usr/local/bin/perl

	#
	# Perl script parse_treefam_bioperl.pl
	# Written by Avril Coghlan ([email protected]).
	# 23-Feb-06.
	#
	# For the TreeFam project.
	#
	# This perl script connects to the MYSQL database of TreeFam families and

avrilcoghlan / treefam_4_genes.pl

Created March 1, 2013 16:31

Perl script that prints out all the genes in a particular TreeFam family.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_4_genes.pl
	# Written by Avril Coghlan ([email protected])
	# 31-Oct-07.
	#
	# For the TreeFam project.
	#
	# This perl script prints out all the genes in a TreeFam-4 family.

avrilcoghlan / treefam_4_losses.pl

Created March 1, 2013 16:33

Perl script that prints out all the gene losses identified in a particular TreeFam family based on the tree for the family.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_4_losses.pl
	# Written by Avril Coghlan ([email protected])
	# 24-Oct-07.
	#
	# For the TreeFam project.
	#
	# This perl script prints out the gene losses in a certain

avrilcoghlan / treefam_dog_man_mouse.pl

Created March 1, 2013 16:35

Perl script that connects to the TreeFam mysql database, and prints out of a list of the TreeFam trees that contain the different possible topologies with respect to the relationship between man, dog, and mouse.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_dog_man_mouse.pl
	# Written by Avril Coghlan ([email protected]).
	# 5-Apr-06.
	#
	# For the TreeFam project.
	#
	# This perl script connects to the MYSQL database of TreeFam families and

avrilcoghlan / treefam_flatworm.pl

Created March 1, 2013 16:39

Perl scrip tthat connects to the TreeFam mysql database, and finds Schistosoma mansoni genes that are single-copy, that have multiple orthologs in most other animals.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_flatworm.pl
	# Written by Avril Coghlan ([email protected]).
	# 30-Jun-06.
	#
	# This perl script connects to the MYSQL database of
	# TreeFam families and finds flatworm genes that are
	# single-copy, that have multiple orthologs in most

avrilcoghlan / treefam_flatworm2.pl

Created March 1, 2013 16:43

Perl script that connects to the TreeFam mysql database, and finds Schistosoma mansoni genes that are multi-copy, but that have just one or two orthologs in most other animals.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_flatworm2.pl
	# Written by Avril Coghlan ([email protected]).
	# 30-Jun-06.
	#
	# This perl script connects to the MYSQL database of
	# TreeFam families and finds flatworm genes that are
	# multi-copy, that have 1 or 2 orthologs in most

avrilcoghlan / gist:5065951

Created March 1, 2013 16:45

Perl script that connects to the TreeFam mysql database, and retrieves within-species Schistosoma mansoni paralogs from the 'ortholog' table of the database.

	#!/usr/local/bin/perl

	#
	# Perl script treefam_flatworm3.pl
	# Written by Avril Coghlan ([email protected]).
	# 30-Jun-06.
	#
	# This perl script connects to the MYSQL database of
	# TreeFam families and finds flatworm paralogous genes.
	#

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