ERaBLE: Evolutionary Rates and Branch Lengths Estimation
ERaBLE is a phylogenomic distance-based method to simultaneously estimate the branch lengths of a given reference topology, and the relative evolutionary rates of the genes employed in the analysis, using a collection of distance matrices (one distance matrix per gene). These distance matrices can either be directly estimated from pairwise alignments of the gene sequences, or they can be calculated from gene trees inferred for each gene.
Downloads
The ERABLE source code, binaries, and datasets are available in the ATGC GitLab repository. Download the software archive for your operating system (Linux or Windows), along with any datasets you need.
Run ERABLE online
ERABLE will also be available to run online through the ATGC platform, allowing you to submit analyses and retrieve results directly from your web browser, without installing the software locally.
Other tools
CompPhy
CompPhy: a web-based collaborative platform for comparing phylogenies CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees. Users can freely manage collections of trees and communicate on a common project. By collaborative, we mean that several users connected to the same project can manipulation at the same time trees from shared…
EPIK: Precise and scalable evolutionary…
EPIK is a program dedicated to « Phylogenetic Placement » (PP) of metagenomic or metabarcoding reads on a reference tree. It is similar in spirit and technically the successor of RAPPAS (Linard et al. 2020). EPIK achieves identical or slightly better accuracy than RAPPAS and outperforms it in speed and flexibility. In many aspects the documentation of RAPPAS…
LoRMA: a self correction program…
Overview LoRMA is an error correction program for long reads, which are sequences obtained using the third generation of sequencing technologies (3GS), either with Oxford Nanopore technology or with Pacific Biosciences technology. LoRMA is a so-called self-correction software, as opposed to e.g. LoRDEC that is a hybrid error correction tool. This means that LoRMA uses…