Genome-wide analyses reveal drivers of penguin diversification
Data files
Aug 17, 2020 version files 4.49 GB
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cds_all.tar.gz
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cds_DNA.tar
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extractUces.pl
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FilterByTaxNumber.py
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FilterUCEs.py
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Introgression-penguins-master.zip
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intron_all.tar.gz
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intron_DNA.tar.gz
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mitogenome_calibrated.log
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mitogenome_calibrated.tree
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mitogenome_calibrated.xml
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mitogenomes_33_alig.fasta
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PNO.zip
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RAxML-NG-Astral-III-master.zip
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scrubReads.pl
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Selection-penguins-master.zip
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transExonCapPhyloV3.3.8.pl
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uce_all.tar.gz
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uce.tar
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UCEs-infile-BEAST.xml
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UCEs-log-BEAST.log
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UCEs-tree-BEAST.tree
Abstract
Usage notes
Submission of all the information related to the manuscript of the penguins phylogenome:
- Genomic data: Intron, CDS, UCE, and Mitogenome alignment files for phylogenetic reconstruction and species tree for all data set and without the yellow-eyed penguin genome; and the final dated phylogeny and the BEAST files for UCE and Mitogenome.
- Scripts: Cleaning raw reads: scrubReads.pl; Extracting UCE markers: extractUces.pl; Performing MSA for introns/cds and cleaning the alignment: transExonCapPhyloV3.3.8.pl; Filtering for UCE: FilterByTaxNumber.py and FilterUCE.py; RaxML_NG_Astral III: laucher.py, makeDirs.py and process_runner.py; Predicted Niche Occupancy: PNO_Rscript.txt; Introgression: CreateDfoil_input.py; Natural selection: runEte3_sitemodel_contigs.sh