A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
Data files
Apr 13, 2021 version files 84.77 MB
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Data_part_1.tar.gz
61.45 MB
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Data_part_2.tar.gz
23.31 MB
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README.txt
3.77 KB
Apr 14, 2021 version files 84.77 MB
-
Data_part_1.tar.gz
61.45 MB
-
Data_part_2.tar.gz
23.31 MB
-
README.txt
3.77 KB
Abstract
Usage notes
DATA PACKAGE FROM Wang ET AL (JOURNAL OF SYSTEMATICS AND EVOLUTION)
A phylogenomic perspective on gene tree conflict 1 and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
This package contains the data and software outputs (i.e. fasta filtes, alignments, trees, etc).
Part 1. File called. Data_part_1.tar.gz
1_alignments. Unaligned fasta files (*.fa), MAFFT aligned fasta files (*.aln), and Cleaned alignments with Phyx (*.aln-cln)
2_trees. RAxML bipartition labeled trees (*.tre), and boostrapt trees (*.trees) from each of the alignments of 1_alignments.
3_masked_mono_para_tips. Trees from 2_trees with masked monophyletic and grades of the same species.
4_masked_spurious_tips. Trees from 3_masked_mono_para_tips with spurious tips removed with TreeShrink. Some *.txt files represent the tips removed byTreeShrink. Empty *.txt means that TreeShrink did not remove any tip from that tree.
5_orthologs
1_final_orthologs. MO orthologs pruned from trees of 4_masked_spurious_tips.
2_fasta_files_from_orthologs. Clean alignments (MAFFT and Phyx) from 1_final_orthologs.
3_concatenated_alignments. Concatenated alignments of the individual clean alignments of 3_concatenated_alignments.
4_gene_trees. RAxML trees from alignments of 3_concatenated_alignments.
5_rooted_trees.
all_rooted. Rooted trees from 4_gene_trees
no_root. Trees without root.
6_analyses
ASTRAL. ASTRAL species trees from all trees from 4_gene_trees
Phylonet
11_taxa
1_fasta_to_tree. Alignments and RAxML trees from the 11-taxa reduced data set.
2_rooted_trees. Rooted trees from 1_fasta_to_tree
3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
7_taxa
1_taxa_to_tree. Alignments and RAxML trees from the 7-taxa reduced data set.
2_rooted_trees. Rooted trees from 1_fasta_to_tree
3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
9_taxa
1_fasta_to_tree. Alignments and RAxML trees from the 9-taxa reduced data set.
2_rooted_trees. Rooted trees from 1_fasta_to_tree
3_analyses. Phylonet results from MPL analyses from 1-5 hybridization events.
Phyparts. Phyparts result from the ASTRAL, RAxML, cpDNA tree.
QuartetSampling.
QS_ASTRAL. QuartetSampling results fo the ASTRAL tree.
QS_cpDNA. QuartetSampling results fo the cpDNA tree
QS_RAxML. QuartetSampling results fo the RAxML tree
RAxML. RAxML tree from the alignment of 3_concatenated_alignments.
If you have any question about data in Data_part_1.tar.gz, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com
Part 2. File called. Data_part_2.tar.gz
baits-Moderate-RM25pc-17056.fas. This file contains the baits designed for Dipsacales.
character_chroloplast_and_nuclear. This folder contains the morphological character coding matrix, and the output of Mesquite for the nuclear and cpDNA data.
cpDNA. This folder contains the cpDNA alignment and the inferred tree with RAxML.
divertime_chroloplast. This folder contains the XML input and nexus files output of the divergence time estimation with BEAST for the cpDNA data.
divertime_nuclear. This folder contains the XML input and nexus files output of the divergence time estimation with BEAST for the nuclear data.
If you have any question about data in Data_part_2.tar.gz, please do not hesitate to contact Hong-Xin Wang at 854616397@qq.com or Huafeng Wang at hfwang@hainanu.edu.cn