SEQanswers

Go Back   SEQanswers > Personalized Genomics > Personalized Genomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to construct phylogenetic tree using SNPs tianyub836 Bioinformatics 10 05-21-2013 06:27 AM
Reference genome-SNP calling melNGS Bioinformatics 0 09-27-2012 03:32 AM
Creating Phylogenetic tree from MAF format file mez Bioinformatics 3 09-04-2012 09:02 AM
phylogenetic tree renesh Bioinformatics 7 03-20-2012 08:24 AM
MAQ vs BWA/SAMTools - differences in SNP calling algorithm? mard Bioinformatics 2 10-20-2010 02:17 PM

Reply
 
Thread Tools
Old 02-18-2013, 10:22 AM   #1
KerryOdair
Senior Member
 
Location: Pacific Northwest

Join Date: Sep 2010
Posts: 123
Default AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications.

The software AMY-Tree (inclusive the WHY-program and the user manual) is freely available on the website bio.kuleuven.be/de/dev (it will be online as soon as the manuscript is accepted). On this website, at least every six months (unless no new data has appeared), an update will be given of the SNP conversion file and of the Updated Y chromosomal phylogenetic tree in tab separated value format based on scientific publications.

Link to provisional PDF:
http://www.biomedcentral.com/content...164-14-101.pdf
__________________
FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a
KerryOdair is offline   Reply With Quote
Old 11-25-2013, 08:15 AM   #2
vivek_
PhD Student
 
Location: Denmark

Join Date: Jul 2012
Posts: 162
Default

I tried using this software on some exome data and it appears to be really slow and memory hogging.

I'd like to know if I can obtain the Y chromosome mutations listed by haplogroup in a machine parse-able format so I can check to see if I can develop a tool with a similar functionality.
vivek_ is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO