File containing contigs in FASTA format from Antecaridina lauensis assembled de novo using Trinity.

Antecaridina lauensis .bed file containing information for putative ORFs as called by the program TransDecoder

Antecaridina lauensis .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder

Antecaridina lauensis .gff file containing mapping information for the putative ORFs as called by the program TransDecoder

Antecaridina lauensis .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder

Antecaridina lauensis transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate

File containing contigs in FASTA format from Caridina rubella assembled de novo using Trinity.

Caridina rubella .bed file containing information for putative ORFs as called by the program TransDecoder

Caridina rubella .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder

Caridina rubella .gff file containing mapping information for the putative ORFs as called by the program TransDecoder

Caridina rubella .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder

Caridina rubella transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate

File containing contigs in FASTA format from Halocaridinides trigonophthalma assembled de novo using Trinity.

Halocaridinides trigonophthalma .bed file containing information for putative ORFs as called by the program TransDecoder

Halocaridinides trigonophthalma .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder

Halocaridinides trigonophthalma .gff file containing mapping information for the putative ORFs as called by the program TransDecoder

Halocaridinides trigonophthalma .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder

Halocaridinides trigonophthalma transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate

File containing contigs in FASTA format from Metabetaeus lohena assembled de novo using Trinity.

Metabetaeus lohena .bed file containing information for putative ORFs as called by the program TransDecoder

Metabetaeus lohena .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder

Metabetaeus lohena .gff file containing mapping information for the putative ORFs as called by the program TransDecoder

Metabetaeus lohena .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder

Metabetaeus lohena transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate

File containing contigs in FASTA format from Metabetaeus minutus assembled de novo using Trinity.

Metabetaeus minutus .bed file containing information for putative ORFs as called by the program TransDecoder

Metabetaeus minutus .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder

Metabetaeus minutus .gff file containing mapping information for the putative ORFs as called by the program TransDecoder

Metabetaeus minutus .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder

Metabetaeus minutus transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate

A compressed file containing 25,742 files that describe 12,871 orthologous clusters. Each cluster has two files associated with it: one of unaligned sequences in FASTA format (ending in .fasta) and one with sequences that were aligned using ClustalO (ending in .fasta_clustalo). Orthologous clusters were generated using ORthoMCL and the putative ORFs from each of the five anchialine shrimp transcriptomes.

A compressed file consisting of 1,784 files describing the 892 orthologous clusters that contained a single ortholog from each of the five anchialine shrimp species. For each orthologous cluster there are two files: one file contains unaligned sequence files in fasta format (ending in .fasta) and one file contains sequences that were aligned using ClustalO (ending in .fasta_clustalo). Orthologous clusters were identified using OrthoMCL and the putative ORFs from the five anchialine shrimp species.

A compressed file consisting of 10 cd hit files (2 for each of the 5 anchialine shrimp species) files used to generate orthologous clusters from the five anchialine shrimp species. One file (ending in .cd-hit_filtered) contains the putative ORFs used to generate clusters while the other file (ending in .cd-hit_filtered.clstr) contains statistics and information on the clusters.

A compressed file consisting of 5 files (1 from each of the five anchialine shrimp species) with the putative ORF amino acid sequences from each species used to generate orthologous clusters.

A compressed file consisting of five Excel spreadsheets (one for each anchialine shrimp species) describing the remapping of raw reads onto the assembled contigs in order to infer expression. There are two spreadsheets per file: the first (name ending in _counts) gives the number of remapped reads (in the Counts column), the length (in the Length column), and the FPKM values (in the FPKM column) for each contig/Trinity subcomponent. The second spreadsheet (name ending in _highExpress) has annotation details for the top 0.1% of highly expressed contigs/Trinity subcomponents.

This bash script will concatenated, digitally normalize, and assemble (via Trinity) paired end .fastq files. See comments for usage, and if script is modified, please provide proper attribution.

This script will generate a Trinotate annotation compressed file for a .fasta Trinity assembly. See comments for usage, and if script is modified, please provide proper attribution.

This script will generate a tab-delimited report from a Trinotate annotation compressed file. See comments for usage, and if script is modified, please provide proper attribution.

This script will generate summary statistics from an assembled Trinity fasta file. See comments for usage, and if script is modified, please provide proper attribution.

This is the first script (of 2) that will generate the OrthoMCL files discussed in the manuscript. See comments for usage, and if script is modified, please provide proper attribution.

This is the second script (of 2) that will generate the OrthoMCL files described in the manuscript. See comments for usage, and if script is modified, please provide proper attribution.

This script will align fasta file (e.g., those generated by OrthoMCL) using ClustalO. See comments for usage, and if script is modified, please provide proper attribution.

This script will map .fastq reads to a .fasta assembly file and generate a tab-delimited table of counts of reads that mapped back to each Trinity subcomponent. See comments for usage, and if script is modified, please provide proper attribution.