Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
De novo genome assembly, phylogenetics, comparative genomics analysis, and functional variant annotation
in depth analysis of heteropecillious sites in supermatrices
Data and Code for the manuscript "Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius"
rRNADif is a method to measure intragenomic 16S rRNA variability within the desired genome sequence against a chosen set of organisms. The app is calculating ML phylogenetic tree and uses mean/median branch length within a set of 16S rRNA as a measure of variability between them
This pipeline give you a concatenated multi alignment of 31 Single Copy Markers from multiple genome assembly for further phylogenetic analysis.
An easy-to-use, beginner-oriented tool to align DNA/RNA or protein sequences, infer an approximately Maximum Likelihood phylogenetic tree from the alignment and visualize it
PhyFocus is a conceptual approach to gene family phylogenetics that emphasizes extensive sequence input to generate broad phylogenies for subsequent refining. Phyfocus was conceptualized by David C. Plachetzki, with pre-release coding by Curtis Provencher.
rRNADif is a method to measure intragenomic 16S rRNA variability within the desired genome sequence against a chosen set of organisms. The app is calculating ML phylogenetic tree and uses mean/median branch length within a set of 16S rRNA as a measure of variability between them
pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies
RAxML agave app and docker image
A comprehensive microbial genomic analysis pipeline that includes quality control, gene prediction, annotation, and comparative genomic analysis for identifying and visualizing key genetic features in microbial genomes.
Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"
Scripts for Hill et al. (2023) doi:10.1093/gbe/evad038 🌿
Agave Docker app for BEAST phylo package
Bioinformatic scripts for working on the UiO Abel compute cluster
MrBayes app w/docker & mpi
Beast 2 agave & docker package
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