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 SciencesHybPiper_artocarpus_analysis.tar.gz 数据集自述文件 artocarpus_trimmed.exon.tar.gz：收录333个基因、28个类群的经过修剪处理的外显子（exon）编码序列比对文件。序列通过MAFFT完成多序列比对，随后使用Trimal进行修剪，剔除了缺失数据占比超过80%的比对列。 supercontig_trimmed_fasta.tar.gz：收录333个基因、28个类群的经过修剪处理的重叠群（supercontig）序列比对文件，其中同时包含外显子（exon）以及侧翼的“splash zone”内含子（intron）序列。序列通过MAFFT完成多序列比对，随后使用Trimal进行修剪，剔除了缺失数据占比超过80%的比对列。 artocarpus_hybpiper_genelengths.txt：记录了采用BWA方法，从28个类群的458个基因座（locus）中召回得到的外显子序列（编码序列CDS，Coding Sequence）的长度。该文件通过HybPiper内置的`get_seq_lengths.py`脚本生成，用于借助`gene_recovery_heatmap.R`脚本绘制HybPiper研究论文中的热图。 allbaitsuppercase.fna：供HybPiper使用的核苷酸“靶标”文件。针对333个基因座，每个基因包含两条直系同源序列（orthologous sequence）：一条来自面包果（Artocarpus camansi）草图基因组，另一条来自桑树（Morus notabalis）基因组；剩余基因仅包含Artocarpus属的直系同源序列。 artocarpus_bwa.supercontig.supermatrix.raxml.tre：基于333个“系统发育”基因座，利用22种Artocarpus属物种与6个外类群（outgroup）的重叠群序列拼接超矩阵（supermatrix）构建得到的RAxML系统发育树。该系统发育树基于核苷酸数据，采用GTRCAT模型构建，每个基因对应一个独立分区。 artocarpus_hybseq.exon.raxml.names.tre：基于333个“系统发育”基因座，利用经HybPiper提取的22种Artocarpus属物种与6个外类群的外显子序列拼接超矩阵构建得到的RAxML系统发育树。节点标签代表200次“快速自举（fast bootstrap）”重复实验得到的自举支持值（bootstrap support）。 本数据集分析源自如下文献： Johnson M.、Gardner E.M.、Shaw J.、Liu Y.、Medina R.、Goffinet B.、Zerega N.J.C. 与 Wickett N.，《HybPiper：利用靶向诱饵捕获技术从高通量测序读段中提取系统发育数据集》，发表于*Applications in Plant Sciences*（《植物科学应用》）。