MOLE-BLAST
MOLE-BLAST searches for closest neighbors... [?]
MOLE-BLAST is a tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple sequence alignment (MSA) between the query sequences along with their top BLAST database hits, and generates a phylogenetic tree. Query sequences in the tree are denoted with highlighted node labels. If the input sequences come from different genes or loci, MOLE-BLAST can cluster them and compute an MSA and a phylogenetic tree for each locus separately.
Enter Query Sequences
(up to 300 input sequences with up to 5000 bases each) [?] Clear
Query sequences to be aligned should be pasted in the text area. Format of the input is automatically determined. To allow this feature there are certain conventions required with regard to the input of identifiers. more...

Choose Search Set
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Align
Advanced parameters
Database Search Parameters
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Select BLAST program for a database search

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Maximum number of aligned database sequences to save.

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Enter an Entrez query to limit the search.

Query Clustering Parameters
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Cluster query sequences to separate different loci.

A cluster is formed from a group of sequences that all yield alignments with one another which satisfy percent identity, and sequence coverage thresholds.

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Minimum percent identity required for a group of sequences to be assigned to the same locus.

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Minimum percentage of a sequence that must be covered by alignments with others required to be included in the same locus.

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Two clusters that share query sequences will be merged and will form a single cluster. The threshold is the minimum size of the intersection between the two clusters as a percentage of the number of elements in the smaller cluster, required for merging these two clusters.

Multiple Alignment Parameters
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Number of database sequences to align with each query.

Align