Table 1 Summary of XplorSeq functionality
Function | Description1 |
|---|---|
Import | Â |
   Chromatogram... | Import DNA chromatograms (.esd, .scf, .abi etc.): phred |
   PHD... | Import DNA sequences in Phd format |
   Contig... | Import DNA sequences and quality scores in FastA format |
   Blast... | Parse Blast records |
   FastA... | Import DNA sequences in FastA format |
   XplorSeq Library... | Import XplorSeq document |
   Phylogenetic Lineage... | Import phylogenetic lineage information from entrez |
   Metadata... | Import metadata in key-value format |
Export | Â |
   Sequences... | Export DNA sequences in variety of formats |
   FastA + Qual... | Export DNA sequences and quality scores |
   Blast Info... | Export summary of Blast records |
   Cluster Table... | Enumerate OTUs belonging to groups of sequences |
   OTU Diversity... | Calculate OTU richness for set of sequences |
   Quality Scores... | Export summary of quality scores |
   Blast Accession #'s... | Export accession numbers of top Blast hits |
   Sequin Script... | Export data in format for Genbank submission (sequin) |
   Blast Database... | Create a Blast database (formatdb) |
   XML File... | Export data in XML format |
   Metadata... | Summarize and export metadata |
   Placeholder Tree... | List selected sequences in Newick format |
Analyze | Â |
   Basecall->Blast... | Pipe data from chromatogram through Blast analysis |
   Contig->Blast... | Pipe data from contig assembly to Blast analysis |
   Basecall... | Perform base calling (phred or ttuner) |
   Contig... | Perform contig assembly (phrap or TIGR_Assembler) |
   Blast NCBI... | Blast query of Genbank |
   Blast Local... | Blast query of local blast database |
   Get Entrez Lineage Info. | Download entrez phylogenetic lineage information (idfetch) |
   Align... | Perform multiple sequence alignment (clustal) |
   Biodiversity (biodiv)... | Calculates biodiversity indices with random resampling (biodiv) |
   XplorSeq Doc Difference... | Generate differences between two XplorSeq documents |
Transform | Â |
   Edit Sequence Names... | Alter names of sequences |
   Edit Lineage Names... | Edit phylogenetic lineage information |
   Edit Metadata... | Edit metadata associated with sequence |
   Edit Metadata Keys... | Edit all metadata keys in document |
   Group... | Group sequences and contigs |
   UnGroup... | Ungroup sequences and contigs |
   Clean... | Delete blast information, contigs |
   Sort... | Sort records in document |
   Set Oligos... | Associate primer sequences with sequence objects |
   Trim... | Trim sequences based on quality score and primer |
   UnTrim. | Remove trimming information |
   Rev.-Complement | Reverse complement sequence |
   DNA -> RNA | Convert DNA sequence to RNA sequence |
   RNA -> DNA | Convert RNA sequence to DNA sequence |
   UPPER CASE | Convert sequence to upper case |
   lower case | Convert sequence to lower case |
Alignment Analysis | Â |
   OTU clustering | Cluster Operational Taxonomic Units (sortx) |
   Clearcut NJ Tree... | Fast neighbor joining trees (clearcut) |
   Phylip distance matrix... | Calculate distance matrix (dnadist) |
   Phylip NJ Tree... | Calculate Neighbor joining or UPGMA trees (neighbor) |
   Phylip seqboot... | Generate bootstrap replicates of alignment (seqboot) |
   Phylip consense... | Generate consensus of multiple trees (consense) |
   RAxML... | Generate Maximum Likelihood tree (raxmlHPC) |