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bam_to_cov_range

A python script to go from bam file to a tab separated file with coverage ranges

catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

cynipoidea_paper

damageplots_from_bam

Generate one PDF with different plots including read length, read % ID PMD scores, Damage plot and Eveness of coverage along the refence genome

dendropy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

edwardslab

Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edwards' bioinformatics lab at SDSU.

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

extract_ncbi_assembly_metadata

filamentous_viral_family_project

gc_content_in_sliding_window

Calculate GC% and GC deviation for circular genomes

genomes_to_msa

Input a table with a list of genome files > output a MSA file aligned with the Sibeliaz ready for phylogenetic analysis (+ RapidNJ tree included)

genoplotr_help

gggenomes

A grammar of graphics for comparative genomics

hgt-finder-between-2-species

ilhabela

R course in Ilhabela, Brazil, June 2015

iq-tree

Efficient phylogenomic software by maximum likelihood

justified

Android TextView or EditText with justified text.

justifiedtextview

JustifiedTextView is an android view that justifies the text. Gives support to older Android versions because "setJustificationMode" was introduced until API 26.

magnet

Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

mesquitecore

The core Mesquite repository

orf-finder-py

Python script utilised for identifying open reading frames in a study of Calliactis polypus regeneration

orthofinder

Phylogenetic orthology inference for comparative genomics

parsing-repeatmasker-outputs

Few scripts facilitating the extraction of info from Repeat Masker .out files

phd

PhD Manuscript

phd_defense

All supplementary files from my PhD defense can be find here

repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

revbayes

Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

text-align

jQuery Text Alignment plugin

treemmer

Python tool to reduce size and redundancy of phylogenetic datasets