Tutorial for using MCMCTree as implemented by Brown Lab at SIUC. For divergence time estimation on UCE datasets, for dendrobatid frogs.
☆10Jun 19, 2020Updated 5 years ago
Alternatives and similar repositories for brownlab-workflow-mcmctree
Users that are interested in brownlab-workflow-mcmctree are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tools to process OrthoFinder output: Calculate the most common gene name of an orthogroup by majority vote and create plots analogous to …☆20Jan 14, 2026Updated 3 months ago
- MCMCtree tutorials☆30May 27, 2024Updated last year
- ☆13Mar 24, 2026Updated 3 weeks ago
- A genome assembly assessment pipeline.☆38Nov 20, 2023Updated 2 years ago
- A Shiny-based framework to analyze and visualize interactively genomic data☆11May 11, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Jan 23, 2026Updated 2 months ago
- NCBI download and Orthofinder analysis☆13Jun 17, 2022Updated 3 years ago
- PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals☆10May 17, 2024Updated last year
- A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria☆19Oct 14, 2020Updated 5 years ago
- Extract information from natural history annotations☆10Apr 3, 2026Updated 2 weeks ago
- Newick tree processing☆13Mar 25, 2026Updated 3 weeks ago
- Tree reconstruction of ancestry using incomplete lineage sorting☆11Jan 9, 2026Updated 3 months ago
- FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignmen…☆35Jun 12, 2024Updated last year
- GeneMiner: a tool for extracting phylogenetic markers from next-generation sequencing data☆12Feb 22, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆46Nov 21, 2019Updated 6 years ago
- Helper scripts for processing and visualization of phylogenetics datasets☆31Feb 19, 2024Updated 2 years ago
- BOSTIn is a new, user-friendly phylogenetic artifact identification package.☆11Mar 28, 2026Updated 3 weeks ago
- LorMe package for R：Lightening One-code Resolving Microbial Ecology Program☆15Jan 13, 2026Updated 3 months ago
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆192Jan 29, 2026Updated 2 months ago
- Methods for the analyses described in Álvarez-Carretero et al. 2022 (https://doi.org/10.1038/s41586-021-04341-1)☆20Dec 15, 2025Updated 4 months ago
- MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function☆12Oct 31, 2025Updated 5 months ago
- ☆18Nov 19, 2025Updated 5 months ago
- RegCloser is a genome gap-closing tool based on the robust regression approach, which is conceptually applicable to de novo assembly of N…☆15Apr 22, 2024Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Phylogenetic penalized likelihood☆55Jun 27, 2025Updated 9 months ago
- Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve o…☆11Jun 19, 2025Updated 10 months ago
- ☆12Jun 12, 2023Updated 2 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- ☆25Mar 27, 2026Updated 3 weeks ago
- ☆16Apr 3, 2023Updated 3 years ago
- Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa☆17Jun 24, 2020Updated 5 years ago
- A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes☆30Apr 10, 2024Updated 2 years ago
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Mar 4, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Nov 20, 2023Updated 2 years ago
- Data analysis of Funannotate and Orthofinder outputs to Pangenome results☆24May 19, 2020Updated 5 years ago
- ☆24Mar 17, 2026Updated last month
- Diploid genome assembly analysis tools☆14Sep 19, 2024Updated last year
- Machuruku☆32Jan 20, 2025Updated last year
- This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new trans…☆20Oct 12, 2025Updated 6 months ago
- Reduction of Althaps and Duplicate Contigs for Improved Downstream Analysis☆20Apr 10, 2026Updated last week