# Comparative Genomics

KBase provides multiple [comparative genomics and phylogenetic analysis Apps](https://kbase.us/applist/#Comparative%20Genomics) to enable researchers to understand evolutionary relationships between organisms and explore structural and functional variance across genomes.

### **Phylogenetic and Taxonomic Analysis**

* [Insert Genome Into Species Tree](https://kbase.us/applist/apps/SpeciesTreeBuilder/insert_set_of_genomes_into_species_tree/release) – Build a phylogenetic tree with your genomes and RefSeq microbial genomes based on conserved orthologous groups
* [Build Microbial Species Tree](https://narrative.kbase.us/#catalog/apps/kb_phylogenomics/build_microbial_speciestree/beta) ([in beta](https://docs.kbase.us/apps/beta)) – Build a phylogenetic tree with your genome and phylum exemplars from RefSeq
* [Build Gene Tree](https://narrative.kbase.us/#catalog/apps/kb_phylogenomics/build_gene_tree/beta) ([in beta](https://docs.kbase.us/apps/beta)) – Build an evolutionary reconstruction tree for a collection of sequence homology related genes
* [Build Phylogenetic Tree with FastTree2](https://kbase.us/applist/apps/kb_fasttree/run_FastTree/release)  – Build a tree with FastTree2 directly on a user-created Multiple Sequence Alignment (MSA)

### Sequence Homology and Functional Analysis

* [BLASTx](https://kbase.us/applist/apps/kb_blast/BLASTx_Search/release), [tBLASTn](https://kbase.us/applist/apps/kb_blast/tBLASTn_Search/release), and [tBLASTx](https://kbase.us/applist/apps/kb_blast/tBLASTx_Search/release) – Search genes in genomes and Annotated Metagenome Assemblies (AMAs) and compare translated protein sequences
* [BLASTn](https://kbase.us/applist/apps/kb_blast/BLASTn_Search/release) – Search genes and AMAs and compare nucleotide sequences
* [BLASTp](https://kbase.us/applist/apps/kb_blast/BLASTp_Search/release) and [psiBLAST](https://kbase.us/applist/apps/kb_blast/psiBLAST_msa_start_Search/release) – Search genes and AMAs and compare protein sequences
* MUSCLE for [nucleotide](https://kbase.us/applist/apps/kb_muscle/MUSCLE_nuc/release) or [protein](https://kbase.us/applist/apps/kb_muscle/MUSCLE_prot/release) sequences – Build and analyze multiple sequence alignments (MSA)
* [HMMER MSA Collection](https://narrative.kbase.us/#catalog/modules/kb_hmmer) – Search and profile genes in genomes and Annotated Metagenome Assemblies (AMAs) with a collection of user-defined MSAs
  * [HMMER Search from MSA](https://kbase.us/applist/apps/kb_hmmer/HMMER_MSA_Search/release) – Search genes in genomes and AMAs with a single user-defined MSA  
  * [HMMER Search with dbCAN2 of CAZy families](https://kbase.us/applist/apps/kb_hmmer/HMMER_dbCAN_Search/release) – Search and profile genes in genomes and AMAs with the suite of CAZy dbCAN2 hidden markov models (HMMs)
  * [HMMER Search for Phylo Markers](https://kbase.us/applist/apps/kb_hmmer/HMMER_PhyloMarkers_Search/release) – Search and profile genes in genomes and AMAs with the suite of GTDB protein phylogenetic marker HMMs
  * [HMMER Search for Env BioElement families](https://kbase.us/applist/apps/kb_hmmer/HMMER_env-bioelement-hmm_Search/release) – Search and profile genes in genomes and AMAs with the suite of Environmental BioElement metabolic families
* [Annotate Domains in a GenomeSet](https://kbase.us/applist/apps/kb_phylogenomics/run_DomainAnnotation_Sets/release) – Compute canonical gene family membership using COG, Pfam, and TIGRFAMs 
* [View Function Profile for Genomes](https://kbase.us/applist/apps/kb_phylogenomics/view_fxn_profile/release) and [View Function Profile for a Phylogenetic Tree](https://kbase.us/applist/apps/kb_phylogenomics/view_fxn_profile_phylo/release) – Examine functional content from canonical domain family annotation
* [Run Fama Genome Profile ](https://kbase.us/applist/apps/FamaProfiling/run_FamaGenomeProfiling/release)– Examine function and taxonomic profiling of microbiomes and functional genes through a similarity search for all predicted proteins in a genome using fast aligner DIAMOND and customized reference protein databases. 

### **Pangenome Exploration** 

* [Compare Two Proteomes](https://kbase.us/applist/apps/GenomeProteomeComparison/compare_two_proteomes/release) – Compare proteomes and produce a synteny map dot plot matrix and table of gene differences
* [Build Pangenome with OrthoMCL](https://kbase.us/applist/apps/PangenomeOrthomcl/build_pangenome_with_orthomcl/release) – Group orthologous protein sequences and identify core and non-core genes across multiple species
* [Calculate Pangenome wiht mOTUpan](https://narrative.kbase.us/#catalog/apps/kb_motupan/run_kb_motupan/release) - Calculate pangenome for microbial genomes, including MAGs of varying quality
* [Compute Pangenome](https://kbase.us/applist/apps/GenomeComparisonSDK/build_pangenome/release) – Build a pangenome and evaluate protein family conservation 
* [Pangenome Circle Plot ](https://kbase.us/applist/apps/kb_phylogenomics/view_pan_circle_plot/release)– View a microbial pangenome as a circle plot using  
* [Compare Genomes from Pangenome](https://kbase.us/applist/apps/GenomeComparisonSDK/compare_genomes/release) – Compare isofunctional and homologous gene families within a pangenome
* [Phylogenetic Pangenome Accumulation](https://kbase.us/applist/apps/kb_phylogenomics/view_pan_phylo/release) – View the pangenome in a phylogenetic context