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alignmentrs

Quickly read and manipulate multiple sequence alignments in Python

alnwrapper

Contains various programs that create sequence alignments.

asite_ip_method

bibmanager

parses a BibTex file (obtain entry type, citekey and other data) and adds citekey to the "note" field.

bseq

Python package for handling biological sequences and alignments

bulkfile-scripts

Scripts useful for working with bulk FlyBase data locally.

conspospy

Python version of conspos package

convert_annotation

Converts input genomic coordinates to the other version of coordinates by referring to mapping table.

cpractice

Collection of codes for learning C programming language.

dnaparswrapper

Estimate parsimonious trees for all alignment files in a given folder using dnapars program in Phylip package.

fsim

simulate mutant allele frequency over generations.

loadlog

Log system-wide CPU temp and load, fan speed, and memory usage. Uses istats and psutil.

nothingspecial

A collection of my Python programs I use everywhere.

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

pathmanage

Makes it easier to deal with tree like folder structure

pausepred_offline

This repository provides the scripts for the PausePred tool. The PausePred is designed to predict translational halts using ribosome footprint density information obtained from ribosomal profiling data.

pdfpropreader

Read properties of PDF files in Python code

refjoin

Join two alignments with referring the identical sequences as template.

rust

treeestimator

Wraps the existing tree estimation programs such as dnapars (from Phylip) and RAxML. Please let me know if you know any good tree estimation program not supported in this package.