This repository has four functions:

1. Host the script that will generate a semi annotated transcriptome from the submitted transcriptomes to NCBI Transcriptome Shotgun Assembly (TSA)
2. Host other scripts used in the analysis of the paper
3. Host the run statistics for the de novo assemblies
4. Link to the data hosted at external locations (NCBI and Data Dryad Repository)

Publication

Reich A., Dunn C.W., Akasaka K., Wessel, G.M. 2015. Phylogenomic Analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS One. 10(3) (Epub ahead of print).

Link to manuscript at NCBI and PLoS One

1. Generate a semi annotated transcriptome

• Click on link for transcriptome of interest (see Table 1)
• Download and unzip the fsa_nt.gz file
• Download and unzip the Master_accs.gz file from this repository
• Run AnnotateTSAfasta.py script (found here)

2. Scripts used in analyses

• Find them here

3. Agalma resource reports for assemblies

• This is the tabular report output of Agalma, which includes the run statistics and resource reports for the individual de novo assemblies (follow internal links).

4. Data hosted at external sites

• NCBI BioProject which includes links to the raw reads in the Short Read Archive
• Data Dryad Repository which includes the constraint trees and supermatrix alignments in phylip format

Table 1