Haruka Yamashita's Projects
Quickly read and manipulate multiple sequence alignments in Python
Contains various programs that create sequence alignments.
parses a BibTex file (obtain entry type, citekey and other data) and adds citekey to the "note" field.
Python package for handling biological sequences and alignments
Scripts useful for working with bulk FlyBase data locally.
Python version of conspos package
Converts input genomic coordinates to the other version of coordinates by referring to mapping table.
Collection of codes for learning C programming language.
Estimate parsimonious trees for all alignment files in a given folder using dnapars program in Phylip package.
simulate mutant allele frequency over generations.
Log system-wide CPU temp and load, fan speed, and memory usage. Uses istats and psutil.
A collection of my Python programs I use everywhere.
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
Makes it easier to deal with tree like folder structure
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.
Read properties of PDF files in Python code
Join two alignments with referring the identical sequences as template.
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.