# # /SSU_rRNA/trees/00README # (June 1, 2001) CONTENTS OF /SSU_rRNA/trees DIRECTORY This directory contains data files in different formats for phylogenetic trees of the small subunit (SSU) ribosomal RNA sequence collections 00Acknowledgements a file attributing the source(s) of data in this directory 00README this file SSU_Euk_rep.newick phylogenetic tree data file for the set of 140 representative eukaryotic sequences with full sequence descriptions in newick format SSU_Euk_rep.printable phylogenetic tree data file for the set of 140 representative eukaryotic sequences with full sequence descriptions in ASCII format SSU_Euk_rep.ps phylogenetic tree data file for the set of 140 representative eukaryotic sequences with full sequence descriptions in PostScript format SSU_Mito.newick phylogenetic tree data file for mitochondrial sequences with full sequence descriptions in newick format SSU_Mito.printable phylogenetic tree data file for mitochondrial sequences with full sequence descriptions in ASCII format SSU_Mito.ps phylogenetic tree data file for mitochondrial sequences with full sequence descriptions in PostScript format SSU_Mito_rep.newick phylogenetic tree data file for the set of 76 representative mitochondrial sequences with full sequence descriptions in newick format SSU_Mito_rep.printable phylogenetic tree data file for the set of 76 representative mitochondrial sequences with full sequence descriptions in ASCII format SSU_Mito_rep.ps phylogenetic tree data file for the set of 76 representative mitochondrial sequences with full sequence descriptions in PostScript format SSU_Mito_short.newick phylogenetic tree data file for mitochondrial sequences with RDP ShortIDs in newick format SSU_Mito_taxnodes.newick phylogenetic tree data file for each taxonomic node from the SSU_Mito.phylo file which contains mitochondrial sequences in newick format SSU_Mito_taxnodes.printable phylogenetic tree data file for each taxonomic node from the SSU_Mito.phylo file which contains mitochondrial sequences in ASCII format SSU_Mito_taxnodes.ps phylogenetic tree data file for each taxonomic node from the SSU_Mito.phylo file which contains mitochondrial sequences in PostScript format SSU_Prok_7.1.newick phylogenetic tree data file for prokaryotic sequences in Release 7.1 with full sequence descriptions in newick format SSU_Prok_7.1_short.newick phylogenetic tree data file for prokaryotic sequences in Release 7.1 with RDP ShortIDs in newick format SSU_Prok_rep_short.newick phylogenetic tree data file for the set of 218 representative prokaryotic sequences with RDP ShortIDs in newick format SSU_Prok_type.newick phylogenetic tree data file for each prokaryotic type strain sequence with full sequence descriptions in newick format SSU_Prok_type_short.newick phylogenetic tree data file for each prokaryotic type strain sequence with RDP ShortIDs in newick format release_8.1_trees directory containing phylogenetic tree data files for Release 8.1 --------------------------------------------------------------------------- Beginning with Release 8.0, a phylogenetic tree containing all sequences in the SSU_Prok alignment file will no longer be generated. Instead, a backbone tree containing 218 representative sequences has been created, and smaller trees of related groups of sequences will be generated and will be contained in the release_8.0_trees. As more trees are created, they will be added periodically. The Release 7.1 phylogenetic trees for small subunit prokaryotic organisms contains 7322 sequences. The phylogenetic tree for small subunit mitochondrial sequences contains 1503 sequences. The SSU_Mito_rep.* phylogenetic tree files (in newick, PostScript, and printable formats) contain 76 sequences. The SSU_Prok_rep_short.newick phylogenetic tree file (in newick format) contains 218 sequences. The SSU_*_taxnodes.* files are phylogenetic trees that include each taxonomic node name which contains at least one rRNA sequence. They are intended to serve as minimalist trees for that alignment, and thus do not include a branch on the tree for each taxonomic node listed in the SSU_*.phylo.headings files. To see the name for the taxonomic node at a higher level than what exists in that particular tree, consult the respective SSU_*.phylo or SSU_*.phylo.headings files. The SSU_Mito_taxnodes.* phylogenetic tree files (in newick, PostScript, and printable formats) contain 210 branches. For sequences in the corresponding tree, they have been numbered to correspond to the order in the complete phylogenetic tree. These numbers are _NOT_ RDP accession numbers. Such index numbers are [#], not [0] as in the SSU_Prok* files. This index number can be used to identify organisms in the respective *.alpha and *.phylo files and vice versa. This number is _NOT_ a permanent, fixed number; it will be different for future trees or even for subtrees created from other trees. ===========================================================================