izziiyt / phylozzii

Branco, Fdur and supportive utility softwares

#Phylozzii

Scaladoc

This repository contains three bioinformatics softwares' source codes.

##Overview

###Fdur

This software is Scala version of Fdur-algorithm implementations. If your data is not so large, you should use the above c++ version implementation alternatively. This software can run on single workstation also on Spark clusters.

###Branco

Branco can assess evolutionary conservation using a phylogenetic tree, a probablistic evolution model and a multiple alignment. Branco outputs expected branch length scores (EBLS) of a target nucleotide. EBLS is statistical expectaion of how long the nucleotide conserved without mutations in phylogenetic tree.

###util

This utility software consists with some supportive functions. With these functions, you can execute deeper analisys or data reformatting to branco's outputs.

##Install & Build

###requirement

####jdk This program is checked running on oracle jdk1.8.0_45 or later. Other jdks are not checked.

####sbt_0.13 or later sbt is a build tool for scala. Installing takes you very long time because of resolving dependency. These depended libraries are cached in your $HOME/.sbt or $HOME/.ivy2 by default and used next time.

###command

put later commands on your terminal

git clone https://github.com/izziiyt/phylozzii
cd phylozzii
sbt assembly

after that, jar files are build at these locations

• phylozzii/branco/target/scala-2.11/branco.jar
• phylozzii/fdur/target/scala-2.11/fdur.jar
• phylozzii/util/target/scala-2.11/util.jar

##Usage

see wiki

##LICENSE

Under the MIT License, see LICENSE.txt

##Reference

• Hisanori Kiryu Sufficient statistics and expectation maximization algorithms in phylogenetic tree models Bioinformatics 27(17), 2346-2353 doi:10.1093/bioinformatics/btr420 (2011)

##Contatct

Yuto Ichikawa : ichikaway{at}cb.k.u-tokyo.ac.jp
Hisanori Kiryu : kiryu-h{at}k.u-tokyo.ac.jp