curcuma_HybSeqProbes_test.fa
test reference containing 100 nuclear exons
Curcuma-roscoeana_plastomeCDS_test.fa
test reference with 11 plastid genes
excludelist.txt
list of samples to remove from alignments
configuration.txt
calibrations for treePL
These scripts are called by main HybPhyloMaker bash scripts.
Use of these scripts should be properly cited, e.g. as follows:
alignmentSummary.R
part of HybPhyloMaker
assembled_exons_to_fastas.py
https://github.com/listonlab/Hyb-Seq_protocol/blob/master/assembled_exons_to_fastas/assembled_exons_to_fastas.py
astral.5.6.1.jar
https://github.com/smirarab/ASTRAL
astralt4.R
part of HybPhyloMaker
catfasta2phyml.pl
https://github.com/nylander/catfasta2phyml
combineboot.py
part of HybPhyloMaker based on http://p4.nhm.ac.uk/tutorial/combine_supports.html
ConsensusFixer.jar
https://github.com/cbg-ethz/ConsensusFixer
CompareToBootstrap.pl
http://meta.microbesonline.org/fasttree/treecmp.html
CompareTree.pl
http://meta.microbesonline.org/fasttree/treecmp.html
fastq2fasta.pl
http://brianknaus.com/software/srtoolbox/fastq2fasta.pl
heatmap.R
part of HybPhyloMaker
histogram.r
part of HybPhyloMaker
HybPhyloMaker_reports.R
part of HybPhyloMaker
LBscores.R
part of HybPhyloMaker and https://github.com/marekborowiec/metazoan_phylogenomics/blob/master/gene_stats.R
MOTree.pm
http://meta.microbesonline.org/fasttree/treecmp.html
mrp.jar
https://github.com/smirarab/mrpmatrix
NEBNext-PE.fa
Oligonucleotide sequences © 2006-2010 Illumina, Inc. All rights reserved.
PhiX.fsa
http://www.ncbi.nlm.nih.gov/nuccore/9626372
plotting_correlations.R
part of HybPhyloMaker and https://github.com/marekborowiec/good_genes/blob/master/plotting_correlations.R
tree_props.r
part of HybPhyloMaker and https://github.com/marekborowiec/good_genes/blob/master/tree_props.R
treepropsPlot.r
part of HybPhyloMaker
TreeCollapseCL4.jar
http://emmahodcroft.com/TreeCollapseCL.html
treePL_wrapper.sh
https://github.com/tongjial/treepl_wrapper
trimmomatic-0.33.jar
http://www.usadellab.org/cms/?page=trimmomatic