v3.0.0 - Fagiolo

This release includes "soibean", a tool designed for the species identification of a pre-analysed ancient environmental DNA sample.

• "soibean" identifies species, a mix of species as well as potential ancestral states of modern references from a FASTQ-file of reads that have been classified to a lower taxonomic resolution (e.g. family level)
• "soibean" uses an MCMC sampling algorithm to find the most likely position on a phylogenetic tree for a species or multiple closely related species in a given sample.
• At the current time, we are restricted to mitochondrial genomes from Tetrapoda and Arthropoda

Please note, if you would like to use euka with the new release, it is necessary to redownload euka's graph files as described in the README.

v2.0.2 - Miritillo

This release fixes minor mistakes in euka's likelihood function for classifying a read and the likelihood function used to compute the MCMC as well as corrections in the README.

v2.0.1 - Mirtillo

This release includes "euka", a tool designed for the rapid and accurate characterization of ancient environmental DNA samples.

It uses a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and uses a maximum-likelihood framework for abundance estimation.
At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions.

v2.0.0 - Mirtillo

This release includes "euka", a tool designed for the rapid and accurate characterization of ancient environmental DNA samples.

• It uses a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and uses a maximum-likelihood framework for abundance estimation.
• At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions.

v1.0.2

Update to the Makefile to reflect changes in VG submodule dependencies.

In particular, the Makefile reverts commits of all VG submodules to avoid any future issues pertaining to changes to the VG codebase.

Mela v1.0.1

Minor fix to HaploCart help message and variable name (no change to the algorithm).

v1.0.0 - Mela

Make the static binary executable:
chmox +x vgan

Docker image: docker.io/gabrielreno/vganv1.0.0