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##  Phylogenetic analysis results from Bista et al. "Genomics of cold adaptations in the Antarctic notothenioid fish radiation".  ##
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Data used for phylogenetic analysis of notothenioid and outgroup fish species, alignments, and phylogenetic trees

The species used for analysis are listed in species.tab, and include 10 outgroups and 31 notothenioid species, 24 sequenced in Bista et al. and 7 published genomes.

Analysis was done with BEAST, IQTREE, and ASTRAL. For details on methods used see description.

Files included:


README			# this file

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alignments
#alignments_full.zip	# alignment files full dataset. Files are named using the name of each BUSCO gene used for analysis.

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BEAST2			# all three datasets (strict, permissive, full) used for BEAST2 analysis
#beast_strict.zip	# BEAST trees from strict analysis. This tree was used for Fig. 2
#beast_permissive.zip	# BEAST permissive dataset
#beast_full.zip		# BEAST full dataset
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#File structure in each of three BEAST folders includes the following files (XXX = dataset)
#XXX.xml: BEAST2 input files
#XXX.trees: Posterior tree distribution estimated with BEAST2
#XXX.log: Posterior distribution of model parameters estimated with BEAST2
#XXX.tre: Maximum-clade credibility summary tree

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astral
#astral.zip		# ASTRAL trees all datasets
# files included in astral.zip are phylogenetic trees generated through astral analysis for each of the strict, permissive, full datasets

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species
#species.tab	# list of species included in analysis

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iqtree
#iqtree.zip	#IQTREE trees all three datasets (strict, permissive, full) 
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#files included in iqtree.zip in three folders (strict, permissive, full)
#concat.treefile : Maximum-likelihood tree with ultrafast bootstrap support values estimated with IQ-TREE for the concatenated dataset
#concord.cf.stat : Concordance factors estimated with IQ-TREE 
#concord.cf.tree : Maximum-likelihood tree with concordance factors estimated with IQ-TREE for the concatenated dataset
#XXX.nex : Input alignment in NEXUS format for IQ-TREE analyses of the XXX (strict, permissive, full) dataset
#loci.treefile : Per-locus maximum-likelihood trees estimated with IQ-TREE for the concatenated dataset