avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_overlaps2.pl
# Written by Avril Coghlan ([email protected]).
# 25-Aug-06.  
#
# For the TreeFam project.
#
# This perl script connects to the MYSQL database of

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script treefam_synteny3.pl
# Written by Avril Coghlan ([email protected])
# 12-Sept-06.  
#
# For the TreeFam project.
#
# This perl script reads in the positions of genes from the TreeFam

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script find_closest_worm_paralogs3.pl
# Written by Avril Coghlan ([email protected])
# 7-Jan-09.   
#
# This perl script finds the pairs of C. elegans paralogs in a family
# that are separated by the least number of edges.

avrilcoghlan

#!/usr/local/bin/perl 
#
# 
# Perl script find_closest_worm_paralogs4.pl
# Written by Avril Coghlan ([email protected])
# 16-Feb-09.   
#
# This perl script finds the bootstrap value for the
# clade containing a pair of C. elegans paralogs in a family (where
# there is no other gene in that clade, ie. they are each other's

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script find_gene_pred_errors1.pl
# Written by Avril Coghlan ([email protected])
# 25-Feb-09.
#
# For the TreeFam project.
#
# This perl script finds cases where two adjacent genes in a species

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script find_treefam_for_schisto_gene2.pl
# Written by Avril Coghlan ([email protected])
# 21-Mar-09.
#
# This perl script reads in a list of Schistosoma genes, and connects
# to the TreeFam mysql database to find out which family they are in.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script find_treefam_with_Ce_Bm.pl
# Written by Avril Coghlan ([email protected])
# 17-Apr-09
#
# This perl script finds TreeFam families that have Ce and Bm genes, and prints out
# how many genes are in the tree.
#

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script get_chroms_from_treefam.pl
# Written by Avril Coghlan ([email protected])
# 9-Sep-09.  
#
# THis perl script reads in a list of 2Ce-to-1Cb orthologs and
# finds cases where the 2 Ce genes are on different chromosomes,
# with one on an autosome and one X-linked.

avrilcoghlan

#!/usr/local/bin/perl

# 
# Perl script get_orthologs7.pl        
# Written by Avril Coghlan ([email protected])
# 29-May-08.  
# Edited 15-Jul-08.
#
# This perl script reads in all trees in TreeFam and finds all
# orthologs between two input species. This parses tree data rather

avrilcoghlan

#! /usr/bin/perl
# Avril Coghlan
# 24-Feb-09
# Perl script to identify singleton genes in a species, defined by genes
# that do not appear in a TreeFam family with any gene from the same species.

use DBI;
use lib "/home/bcri/acoghlan/perlmodulesAvril/"; # edit to point to the TreeFam perl api xxx
use Treefam::DBConnection;