The taxonomic assignation was carried out using the following programs: 1) PhymmBL[ 41] was optimized using the Combine files boolean option in two separated iterations to create both joint and separate IMMs.
To test the differential expression of these novel isoforms, Cuffdiff analyses were performed using the combined transcript files as the reference genome.
Because the replicates of the same sex were highly correlated (supplementary table S1, Supplementary Material online), the triplicate RNA-seq data from each sex were combined as one single fastq file and the average RPKM values from the combined files were used for the following analysis.
Save the newly combined file.
Phylogenetic estimates using ML were performed using both the combined, unpartitioned dataset as well as the combined dataset partitioned by locus (Additional file 2: Table S2).
Click the merge button to get a combined file.
The AS events in young fruits at 2, 5 and 10 dpa were combined using the merged GTF file from the mapped fruit-derived reads.
Profiles were generated using the Matrix file from computeMatrix in profiler, combining both regions plotted on the same plot.
BSP were drawn with Tracer using linear change mode and the combined tree file.
Start Command Prompt using the batch file.
