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# CONCATENATION of ALIGNMENTS / SEQUENCES

- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## DESCRIPTION

### With the help of 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 new name for the newly created concatenated alignment in the field "New Alignment Name" (Make sure that the new alignment name starts with "ali_.....").

### Use "Sequence Type" button to load 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 actual concatenation.

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

### Use "Alignment Separator" to specify the tag/separator between the alignments to be concatenated.

### Pressing CONCATENATE button performs concatenation function for the alignments selected in the order of the alignments present in the "Alignments to be concatenated" list.

### Use MERGE SIMILAR SPECIES button to create new species by merging similar species (for e.g., Similar species having different sequence alignments). Additionally, you can do the same from the "Species" menu clicking on "Merge Similar Species" item.

### If the database contains similar species with different sequence alignments use "MERGE and 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

### None

## WARNINGS

### None

## BUGS

### No bugs known