Analyses from Johnson et al. 2016

README for HybPiper_artocarpus_analysis.tar.gz

artocarpus_trimmed.exon.tar.gz

Trimmed coding sequence (exon) alignments for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data.

supercontig_trimmed_fasta.tar.gz

Trimmed supercontig sequence alignments (containing both exons and flanking "splash zone" intron sequence) for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data.

artocarpus_hybpiper_genelengths.txt

Lengths of exon sequence (CDS) recovered for 458 loci for 28 taxa using the BWA method. File generated using "get_seq_lengths.py" in HybPiper, and used to generate the heatmap figure in the HybPiper manuscript (with "gene_recovery_heatmap.R")

allbaitsuppercase.fna

Nucleotide "target" file used with HybPiper. For 333 loci, there are two orthologous sequences per gene: one from the Artocarpus camansi draft genome, and one from the Morus notabalis genome. For the remaining genes, only an Artocarpus ortholog is present.

artocarpus_bwa.supercontig.supermatrix.raxml.tre

RAxML phylogeny generated from a concatenated supermatrix of supercontig sequences for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Tree generated from nucleotide data using the GTRCAT model, with one partition per gene.

artocarpus_hybseq.exon.raxml.names.tre

RAxML phylogeny generated from a concatenated supermatrix of exon sequences extracted by HybPiper for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Node labels indicate bootstrap support from 200 "fast bootstrap" replicates.

Analyses from: Johnson M., E.M. Gardner, J. Shaw, Y. Liu, R. Medina, B. Goffinet, N.J.C. Zerega, and N. Wickett. HybPiper: extracting phylogenetic datasets from high-throughput sequencing reads using targeted bait capture. Applications in Plant Sciences