The Brown Lab

Disclaimer :: Use at your own risk :: Disclaimer

Some require that you have Biopython installed.

FastQ_Pattern.py -- looks for a sequence pattern of interest, using a grep based approach, in a Fastq run file. It will collect all reads matching the pattern. Then, the script will collect the mate for that read in the other file of a paired-end run. For use with MiSeq or HiSeq Illumina sequence data.

VisualizePhylipMatrix.py -- Makes an R-readable csv file from any phylip file (Nucleotide or Amino Acid). The prerequisites are 1) R and 2) gplots installed in R.

MORE TO COME

Data
Brown MW, Sharpe SC, Silberman JD, Heiss A, Lang BF, Simpson AGB, Roger AJ. 2013. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts.Proceedings of the Royal Society B: Biological Sciences 280: 20131755.

• TarBall with all 159 single gene alignments (unmasked and masked) and single gene trees. See the Supplemental Table S1 for taxon abbreviations.
• TarBall with the supermatrices used in the analyses. 159 gene matrix with 68 or 23 taxa. The included log files provide the depth of matrix coverage per taxa. See the Supplemental Table S1 for taxon abbreviations.
• NCBI Short Read Archive SRX246005. Our Trinity:Inchworm assembly with all clusters over 150bp can be downloaded here.
• Integrin Adhesome data can be downloaded here.
• For the any other dataset used in the analyses please contact me.

• TarBall with all 159 single gene alignments. See the Supplemental Table S1 for taxon abbreviations. The alignments are not masked, but the sites that were used are displayed in the alignments as a “*”. To parse out the masked alignments you can use alvert.py.
• TarBall with the supermatrix used in the analyses. The included log files provide the depth of matrix coverage per taxa. See the Supplemental Table S1 for taxon abbreviations.

• Our Mira and Newbler assembly with all clusters can be downloaded here.

• For the any other dataset used in the analyses please contact me.