Archive for the ‘Epos News’ Category

Tutorial: Merging Alignments and RaxML Multi-Gene analysis

In this tutorial we will create two alignments and perform a multi-gene analysis using RaxML. To get things started lets fetch data from the NCBI. I randomly picked 5 Taxa from “A multigene phylogeny of the Dothideomycetes using four nuclear loci” for the SSU and LSU regions. Start Epos and go to File->New->Fetch from GenBank. […]

Tutorial: Add Cluster support

The Epos framework supports the direct integration of compute clusters based on the Sun Grid Engine. Integrating a remote cluster allows you to submit all jobs directly to the cluster and fetch results later. For this to work, you need SSH access to a remote machine that is part of the cluster. The machine must […]

Tutorial: NAD5

This is a mini-tutorial based on an example from “Gene und Stammbaeume” by Volker Knoop and Kai Mueller. We will use Epos to create a Phylogeny of Marsupials based on the NAD5 Gene. The basic steps involved are: Collect initial data from the NCBI, search for homologue Sequences not covered by the initial search, find […]

Epos 0.9

Finally

Epos 0.9 SNAPSHOT Release

Okey, here is the beta release for version 0.9. New user interface, new modules, integrated blast viewer and taxonomy support. Please keep us informed about anything that is not working properly … and note that we are still heavily working on the tree comparator and taxon modules. Epos 0.9 beta for Windows Epos 0.9 beta […]

Epos Blast Viewer

We just put the epos blast viewer online, as a standalone webstart application on top of the epos framework. The app is small tool that is able to read NCBI blast results from XML files and display the data. You can directly download the sequence and store them on disk and you can export the […]

IntelliJ class cloud

I was bored and played around in IntelliJ, which is open sourced now. I found the analyze class cloud button and here is the result for the Epos sources. Looks like ComponentUtils is an important class

GroovyShell and interactive scripting

Johannes contacted me this weekend and asked about the GroovyShell in the new Epos release, so I decided to create a small screencast that demonstrates the functionality. Get the latest Flash Player to see this player. [Javascript required to view Flash movie, please turn it on and refresh this page] The Epos GroovyShell can be […]

Epos Alvarius

After a few month we are getting closer to a new Epos release – Epos 0.9 Alvarius. We used a branch of the main epos trunk for the development, but now, as we are getting closer to the release, it was time to move everything back into the main branch and set a a new […]

Almost done

The new website almost looks like the old one – which is good. We have to re-upload the screenshots, though. But I think I will use the opportunity to take a few new shots to reflect the development within the EPoS UI. Ok, at least one is already online !