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ratite-genomics

Scripts and other material for the assembly and analysis of ratite genomes.

reciprocal_smallest_distance

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.

rerconverge

Analysis of convergence between organismal traits and DNA/protein sequences

sample

sanpolya

scripts

scripts_irb

shifted-hamming-distance

Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf

silva2014_rustphylogenomics

The set of scripts used in Silva et al. 2014 "Genomic patterns of positive selection at the origin of rust fungi"

smcpp

SMC++ infers population history from whole-genome sequence data.

smith-waterman_viterbi

"Smith-Waterman alignment of two sequence, can be DNA or amino acids" "Also known as viterbi finding the maximum likelihood path of hidden states of a hidden Markov model (HMM)"

speech_recognition

A simple speech recognition using HMM (python)

squeezemeta

A complete pipeline for metagenomic analysis

starbeast3

stokepy

Stochastic models library for Python

stringtie

Transcript assembly and quantification for RNA-Seq

swamp

Sliding Window Alignment Masker for PAML

sweepversustraitoptimum

SweepVsTraitOptimum

sysu_notebook

本项目分享了本人在中山大学数据科学与计算机学院计算机科学专业的课程资料、笔记、回忆和整理的期末考试卷、及课程作业。希望对你们有所帮助❤️，如果喜欢记得给个star哦🌟

thinkbayes

Code repository for Think Bayes.

traveling-salesman-mcmc-approach

Markov Chain Monte Carlo (MCMC) practice

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

treetime_examples

A collection of documented examples using TreeTime

tripal_go

go enrichment for tripal

virsorter2

customizable pipeline to identify viral sequences from (meta)genomic data

xgcode

A server for a collection of web-accessible python scripts.

xpclr

Code to compute the XP-CLR statistic to infer natural selection