Teleost species-tree analyses without fossil constraints
- BEAST input file: 101g_nucl_conc_unconst.xml
- BEAST log file: 101g_nucl_conc_unconst.combined.log.gz
- BEAST MCC tree file: 101g_nucl_conc_unconst.combined.tre
- BEAST posterior tree distribution file: 101g_nucl_conc_unconst.combined.trees.gz
- List of taxon ids: taxa.txt
Teleost species-tree analyses with 28 fossil constraints (using Cretatriacanthus guidottii for Tetraodontiformes)
- BEAST input file: 101g_nucl_conc_28bfossils.xml
- BEAST log file: 101g_nucl_conc_28bfossils.combined.log.gz
- BEAST MCC tree file: 101g_nucl_conc_28bfossils.combined.tre
- BEAST posterior tree distribution file: 101g_nucl_conc_28bfossils.combined.trees.gz
Teleost species-tree analyses with 28 fossil constraints (using Plectocretacicus clarae for Tetraodontiformes)
- BEAST input file: 101g_nucl_conc_28afossils.xml
- BEAST log file: 101g_nucl_conc_28afossils.combined.log.gz
- BEAST MCC tree file: 101g_nucl_conc_28afossils.combined.tre
- BEAST posterior tree distribution file: 101g_nucl_conc_28afossils.combined.trees.gz
RH1 gene-tree analyses
- Nucleotide sequence alignment: rod_opsin.nex
- BEAST log file: rod_opsin.log.gz
- BEAST MCC tree file: rod_opsin.tre
- BEAST posterior tree distribution file: rod_opsin.trees.gz
Diretmus RH1 nucleotide sequences
- Diretmus RH1 sequences: diretmus_rod_opsin.fasta
- Diretmus RH1 sequences including pseudogenes: diretmus_rod_opsin_incl_pseudogenes.fasta
- Diretmus RH1 sequences with upstream region: diretmus_rod_opsin_with_upstream.fasta
Atomistic RH1 modeling
- Protein sequence alignment: rod_opsin_atomistic_modeling.nex
- RH1 gene tree: rod_opsin_atomistic_modeling.tre
- Movie 1: movie_1.mp4
- Movie 1 (small): movie_1_small.mp4
- Movie 1 (preview): movie_1.png
- Movie 2: movie_2.mp4
- Movie 2 (small): movie_2_small.mp4
- Movie 2 (preview): movie_2.png
