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