This App allows a user to construct a species tree using a set of 49 core, universal genes defined by COG (Clusters of Orthologous Groups) gene families. It combines the genome(s) provided by the user with a set of closely related genomes selected from the public KBase genomes import of RefSeq. Since the number of genomes available in KBase is very large, the procedure starts by selecting a subset of public KBase genomes closely related to the user-provided genomes. Relatedness is determined by alignment similarity to a select subset of 49 COG domains. Next, the user genome(s) are inserted into our curated multiple sequence alignment (MSA) for each COG family. The curated alignments have been trimmed using GBLOCKS to remove poorly aligned sections of the MSA. The MSAs are then concatenated. Then, a phylogenetic tree is reconstructed using , (version 2.1.10, a method to quickly estimate approximate maximum likelihood phylogeny, see Publications) with the genome(s) provided by the user and the set of genomes identified as similar in the previous step. FastTree2 is used with the -fastest setting.

Note: when inserting one or more genomes into a species tree, the inserted genomes that are also contained within the KBase list of species will be duplicated in the tree. One copy will have the KBase list ID and the other will have the ID of the inserted genome.

The Neighbor public genome count parameter will control how many nearby genomes are included in the species tree for each input genome. The maximum number of nearby genomes is 200. This represents the total number of close genomes that will be added to the tree. If you have several diverse input genomes, you should increase this number.

The primary output of this object will be a species tree data object. The App report will show the resulting tree and contain links for downloading the tree in newick format and as a pdf or png. Tree leaves are labeled by the NCBI RefSeq species name plus their GCF identifiers. User genomes are labeled with the data object name. Branch support values are shown for each node, as described in the FastTree2 documentation.

This App also creates a Genome Set object containing all the genomes in the species tree that was generated. You must provide a name for this output object. By default, the genomes in this Genome Set are not copied into your narrative, in order to make further analyses (e.g., viewing, finding domains) more convenient, you may select the Copy public genomes to your workspace option. However, this is not recommended if you set a large value for the Neighbor public genome count.

By clicking on the Genome Set object that is generated, you can edit the set of genomes, e.g., to exclude some of them from downstream analyses.

Team members who developed & deployed algorithm in KBase: Roman Sutormin. For questions, please contact us.

The COGs domains used in the estimate of relatedness include:

COG0012	COG0012	Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis].
COG0013	AlaS	Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
COG0016	PheS	Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis].
COG0018	ArgS	Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
COG0030	KsgA	Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis].
COG0041	PurE	Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism].
COG0046	PurL	Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism].
COG0048	RpsL	Ribosomal protein S12 [Translation, ribosomal structure and biogenesis].
COG0049	RpsG	Ribosomal protein S7 [Translation, ribosomal structure and biogenesis].
COG0051	RpsJ	Ribosomal protein S10 [Translation, ribosomal structure and biogenesis].
COG0052	RpsB	Ribosomal protein S2 [Translation, ribosomal structure and biogenesis].
COG0072	PheT	Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis].
COG0080	RplK	Ribosomal protein L11 [Translation, ribosomal structure and biogenesis].
COG0081	RplA	Ribosomal protein L1 [Translation, ribosomal structure and biogenesis].
COG0082	AroC	Chorismate synthase [Amino acid transport and metabolism].
COG0086	RpoC	DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription].
COG0087	RplC	Ribosomal protein L3 [Translation, ribosomal structure and biogenesis].
COG0088	RplD	Ribosomal protein L4 [Translation, ribosomal structure and biogenesis].
COG0089	RplW	Ribosomal protein L23 [Translation, ribosomal structure and biogenesis].
COG0090	RplB	Ribosomal protein L2 [Translation, ribosomal structure and biogenesis].
COG0091	RplV	Ribosomal protein L22 [Translation, ribosomal structure and biogenesis].
COG0092	RpsC	Ribosomal protein S3 [Translation, ribosomal structure and biogenesis].
COG0093	RplN	Ribosomal protein L14 [Translation, ribosomal structure and biogenesis].
COG0094	RplE	Ribosomal protein L5 [Translation, ribosomal structure and biogenesis].
COG0096	RpsH	Ribosomal protein S8 [Translation, ribosomal structure and biogenesis].
COG0097	RplF	Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis].
COG0098	RpsE	Ribosomal protein S5 [Translation, ribosomal structure and biogenesis].
COG0099	RpsM	Ribosomal protein S13 [Translation, ribosomal structure and biogenesis].
COG0100	RpsK	Ribosomal protein S11 [Translation, ribosomal structure and biogenesis].
COG0102	RplM	Ribosomal protein L13 [Translation, ribosomal structure and biogenesis].
COG0103	RpsI	Ribosomal protein S9 [Translation, ribosomal structure and biogenesis].
COG0105	Ndk	Nucleoside diphosphate kinase [Nucleotide transport and metabolism].
COG0126	Pgk	3-phosphoglycerate kinase [Carbohydrate transport and metabolism].
COG0127	COG0127	Xanthosine triphosphate pyrophosphatase [Nucleotide transport and metabolism].
COG0130	TruB	Pseudouridine synthase [Translation, ribosomal structure and biogenesis].
COG0150	PurM	Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism].
COG0151	PurD	Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism].
COG0164	RnhB	Ribonuclease HII [DNA replication, recombination, and repair].
COG0172	SerS	Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
COG0185	RpsS	Ribosomal protein S19 [Translation, ribosomal structure and biogenesis].
COG0186	RpsQ	Ribosomal protein S17 [Translation, ribosomal structure and biogenesis].
COG0215	CysS	Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis].
COG0244	RplJ	Ribosomal protein L10 [Translation, ribosomal structure and biogenesis].
COG0256	RplR	Ribosomal protein L18 [Translation, ribosomal structure and biogenesis].
COG0343	Tgt	Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis].
COG0504	PyrG	CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism].
COG0519	GuaA	GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism].
COG0532	InfB	Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis].
COG0533	QRI7	Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones].