create a custom map with only some countries labeled

In the Run tool Kalign or MAFFT dialog uncheck Quiet mode to see how job is running and add local path to the aligner executable (should be downloaded and installed before, see more explanation in the Multiple Sequence Aligners manual). In Run Tool dialog find section “Multiple Sequence Aligners” and select Kalign or MAFFT (alignment construction by MAFFT for the current set takes less than a minute, by Kalign - 10-15 min): To create multiple alignment, select all accessions in the project ( Shift+click) and select Run Tools option in the context menu or upper panel.

Sequences can be uploaded into project from fasta file as well (see Multiple Sequence Aligners manual). Let add NC_045512(China), MT748758(Italy), MT655135(Spain), MT637143(Russia) via File/Open/Data from GenBank (copy and paste: NC_045512, MT748758, MT655135, MT637143), click Next/Add to an existing Project/Finish.įind newly added genomes at the end of the list of accession in the project. If you want to add some other complete covid19 genomes and know genome accession numbers, they can be added to the same project directly from GenBank. See all accessions were added to the newly created project. Select all of them using Shift+click, open right click context menu and Add to Project/Create a new Project. Search returns complete genomes for covid19 currently collected in state Maryland (75, as for ).

In Genome Workbench open Search View, for Search Tool select “Search NCBI Public Databases”, for NCBI Database select 'Nucleotides', in search box add query: 'Severe acute respiratory syndrome coronavirus 2' AND 'complete genome' AND 'USA: MD' and hit Start. Sequences can be added into Genome Workbench project from search result, uploaded from GenBank by accessions, or uploaded from FASTA file. Please use the sample project to follow this tutorial. Database of Single Nucleotide Polymorphisms (dbSNP)Ĭreating phylogenetic tree in Genome Workbench from search.Database of Genomic Structural Variation (dbVar).Online Mendelian Inheritance in Man (OMIM).Database of Genotypes and Phenotypes (dbGaP).Structure (Molecular Modeling Database).Conserved Domain Search Service (CD Search).BLAST (Basic Local Alignment Search Tool).

Create a custom map with only some countries labeled