ytabatabaee

viral-mutation

Language modeling of viral evolution

ASTER

Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

TreeSwift

TreeSwift: Fast tree module for Python 3

DCNet

DCNet — Denoising (DNA) Sequence With a LSTM-RNN and PyTorch & Neural DBG

Algorithms_Design

دوره‌ی طراحی و تحلیل الگوریتم‌ها، برای دانشجویان

data-science-sequencing.github.io

Web site for the class EE 372 : Data Science for High-Throughput Sequencing at Stanford

Data_Structures_Algorithms

دوره‌ی داده‌ساختارها و مبانی الگوریتم‌ها، برای دانشجویان

machina

Framework for Metastatic And Clonal History INtegrative Analysis

SimPhy

SimPhy: A comprehensive simulator of gene family evolution

root_digger

A tool to root phylogenies

MinVar-Rooting

Linear-time rooting of phylogenetic trees

mp-est

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function

Deep-Learning-Material

Notebooks for Deep Learning course (CE719) TA sessions - Sharif University of Technology

ASTRID

Fast, accurate species tree estimation.

STRIDE

STRIDE: Species Tree Root Inference from Gene Duplication Events

DISCO

Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve orthologs and discard paralogs.

SVDquest

cm_pipeline

Pipeline that uses an improved version of CM for generating well-connected clusters

tyranni

Code used to assemble and analyze a phylogeny of suboscine birds (Aves; Tyranni)

GTM

Guide Tree Merger

PhySigs

Phylogenetic inference of exposures of mutational signatures