25 research outputs found
DNA alignments
cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files
CDS translations
Corresponding CDS sequences for the peptide translations. These are multifasta files
alignments for other WGD tests
Alignments of orthogroups used to look at putative WGD events in data set. These are multifasta files
peptide translations
Peptide translations based on a blastx of the filtered Trinity assemblies to the 22 genome dataset (Amborella Genome Consortium, 2013) and conceptually translated using Genewise. These are multifasta files
concat_alllegume.fsa
Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file
trees - bipartitions
The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files
RAxML_bipartitions.concat_alllegume.fsa.raxml.out
RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file
Legume pairs - ksplots
Putative paralog pairs estimated from Ks plots for multiple species from study. These were used to test for other WGD events (other than PWGD). This is a tab delimited file with the first and second columns being Ks plot identified putative paralogs and the third column being a designation for the putative event
assemblies
The filtered (>1% per-component read representation) Trinity assemblies of legume transcriptomes used in this study, as part of the Thousand Plant Transcriptome (1kp) project. These are multifasta files
trees for other WGD tests
RAxML best trees with bootstrap values added (bipartitions) for orthogroups used to test for putative WGD events in data set identified through Ks plots that are not PWGD. These are Newick tree files