bioinformatics 46 python 38 evolution 25 genomics 17 biology 16 phylogeny 14 phylogenomics 12 visualization 11 phylogenetic-trees 10 tree 9 taxonomy 8 orthology 8 sequence-alignment 6 phylogeography 6 newick 6 genetics 6 biopython 6 alignment 6 computational-biology 6 molecular-evolution 5 orthology-inference 5 population genetics 5 evolutionary-biology 4 pbs 4 pandas 4 comparative-genomics 4 microbial-genomics 4 nexus 4 protein 4 dna 4 maximum-likelihood 3 contact tracing 3 science 3 visualisation 3 algorithms 3 matplotlib 3 splitstree 3 pytorch 3 Bayes 3 variational 3 phylodynamics 3 machine-learning 3 orthologues 3 tree-structure 3 phylogenomic 3 fast 3 orthologs 3 birth-death model 3 statistics 3 data-science 3 single-cell 3 pipeline 3 systematics 3 evolutionary 3 protein-structure 3 simulation 2 qsub 2 ncbi 2 ftp 2 blast 2 biosql 2 qiime 2 variational-inference 2 gui 2 cancer 2 single cell 2 tumor phylogeny 2 orthology-assignments 2 newick-format 2 timetree 2 numpyro 2 jax 2 c-plus-plus 2 statistical-methods 2 torchtree 2 paup 2 supertree 2 shell 2 sge 2 microbiome-analysis 2 microbiome 2 metagenomics 2 bacteria 2 hpc 2 cross-platform 2 16s 2 microbiology 2 16S 2 PASTML 2 microbial ecology 2 treeview 2 tree comparison 2 tree visualization 2 tree reconstruction 2 QIIME 2 phylogenetic-analysis 2 mrbayes 2 beast2 2 phylogenetic trees 2 phyloinformatics 2