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#Overview This repository aims to host a set of Python scripts that will simulate transcriptomes with known orthology/paralogy relationships, gene tree topologies, and species tree topologies. It will incorporate a summary statistics script for assessing phylogenetics program performance at the homolog clustering level and at the final tree reconstruction level. #Testing To test, simply run: python simulate.py -p params.txt #Pipeline Organization ##Species and Gene Tree Simulation Species and gene tree simulation is done based off [SimPhy](https://github.com/adamallo/SimPhy). ##Sequence Simulation Sequence simulation for each gene tree is further done based off [indel-seq-gen](http://bioinfolab.unl.edu/~cstrope/iSG/) with root sequence input from assembled transcriptomes from the gastropod project. ##Read Simulation Read simulation for each gene sequence, sorted by taxa is done using [RNASeqReadSimulator](https://github.com/davidliwei/RNASeqReadSimulator). ##Homology Assessment Homology clustering is performed using either fablast and mcl or blastp and mcl from the [agalma](https://bitbucket.org/caseywdunn/agalma) package. Homology assessment has yet to be determined.