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Last update on 25. Nov 2018 .
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Concatenation of alignments/sequences

DESCRIPTION

With the help of the concatenation function, one can concatenate the aligned sequences, which are contained in the same species preserving the ALIGNMENT. Before using concatenation function make sure that the species contains more than two aligned or unaligned sequences.

Specify a name for the newly created concatenated alignment in the field "New alignment name".

Use "Sequence Type" button to display the desired type of alignments/sequences from the database.

Use Arrow buttons (located in between the lists) to select or remove the alignments into/from the "Alignments to be concatenated" list.

You can also rearrange the order of concatenation of alignments by using "up" and "down" arrow keys (located by the side of "Alignments to be concatenated" list) before performing the actual concatenation.

Pressing CLEAR LIST button clears the alignments list selected for concatenation.

Use "Alignment Separator" to specify the tag/separator to be inserted into the target sequence data between the data of the alignments to be concatenated.

Pressing the "CONCATENATE" button performs a concatenation of the alignments selected in the order given in the "Alignments to be concatenated" list.

Use the "MERGE SIMILAR SPECIES" button to create new species by merging similar species (for e.g., similar species having different sequence alignments). This function is also available from the Species menu. See ´Merge Similar Species´ for details.

If the database contains similar species with different sequence alignments use "MERGE & CONCATENATE" button to generate new species by merging similar species in the database and concatenating the different sequence alignments contained in the newly merged species.

 

NOTES

If problems occurs during "Merging similar species" and/or "Concatenation", try the following -

  1. Search the database for the "merged_species" field and mark the listed species, if any, and delete them.
  2. Then search the database for the <criterion_field> to use for merging similar species. Mark the resulting species and perform merging similar species.
  3. Usually newly generated (merged) species are marked and use the same to perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT coinside with the selected alignments (names) to be concatenated!

 

EXAMPLES

 

WARNINGS

None

 

BUGS

No bugs known