Markers Database download change

The markers database has moved to a new location.
This will NOT get automatically downloaded. The automatic download will not work until we release a code fix.

You can download the markers from the following link for now and extract to the location of your choice. By default, PhyloSift will look in the following directory ~/share/phylosift. This path can be modified in the phylosiftrc file.
https://doi.org/10.6084/m9.figshare.5755404.v4

Sorry for the inconvenience.

PhyloSift paper selected for the PeerJ Picks 2014 Collection

We’re honored that the software paper describing the PhyloSift pipeline has been selected for inclusion in the PeerJ Picks 2014 Collection:

This Collection celebrates the one-year anniversary of PeerJ publishing their first articles. Staff combed through the 500 articles published so far in both PeerJ and PeerJ PrePrints, and picked out 20 personal highlights which represent the scope and diversity of the articles we have published to date. Some articles have over 25,000 views; some already have a significant number of citations; some represent major new findings; some are important papers in open data and open science; some of the PrePrints have multiple revisions; and some are just plain fun! (description from PeerJ’s website)

Click here to browse all the articles selected as 2014 PeerJ Picks

PhyloSift paper now published in PeerJ

We’re delighted to announce the first paper describing the PhyloSift pipeline, published today in PeerJ. In addition to the paper itself, the manuscript reviews are also public (you can read them here – many thanks to Nick Loman and our anonymous reviewers for their help and insight):

Darling AE, Jospin G, Lowe E, Matsen FA IV, Bik HM et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 http://dx.doi.org/10.7717/peerj.243

Please read, discuss, and enjoy!