Concatenate genes
Join FASTA records into one sequence, with an optional linker and a partition table.
Join FASTA records into one sequence, with an optional linker and a partition table.
The In order tab takes every record in the input and joins it to the next one, in the order you pasted them, and gives back a single record. It is the quick way to build a fusion construct out of its parts, to stitch contigs into one scaffold, or to glue an alignment back together after it was split. Whitespace, line breaks and position numbers are ignored, and gaps are kept, so an alignment survives the trip unchanged.
The partition table under Details gives the first and last position of every part in the joined sequence, plus the same information as partition lines a phylogenetics program can read. Those numbers are the only reliable way back: once the parts are joined, nothing in the sequence itself says where one ended and the next began.
Choose a linker and it goes between every pair of neighbouring records, never at the start or the end. The presets cover the common cases:
| Linker | Sequence | Length | Used for |
|---|---|---|---|
| GGGS | GGCGGCGGCTCC | 12 bp | A short flexible linker between two protein domains |
| GGGGS | GGTGGCGGTGGCTCT | 15 bp | The classic flexible linker, often repeated two or three times |
| RBS | AGGAGG | 6 bp | A Shine-Dalgarno sequence before the next gene in an operon |
| Stop | TAA | 3 bp | Ending one open reading frame before the next starts |
| BamHI | GGATCC | 6 bp | Leaving a cut site between the parts |
| 10 Ns | NNNNNNNNNN | 10 bp | A gap of unknown sequence between two contigs |
For a protein fusion, keep every linker a multiple of three bases so the next domain stays in frame, and take the stop codon off every part except the last. Check the finished construct with the DNA to protein translator, and its cut sites with the restriction site finder.
Type record numbers into the Reverse complement field and those records are flipped before they are joined. Single numbers, a list and a range all work: 2, 1, 3or 2-4. Use it when a contig or a sequencing read came off the other strand. To flip everything instead, use the reverse complement tool.
The By name tab does the concatenation a multi-gene phylogeny needs: one aligned sequence per taxon, holding every gene in order. Paste the gene alignments one after another in a single FASTA, in the order you want the partitions:
"Try an example" on In order loads three parts, a 54 bp signal peptide, 120 bp of the EGFP coding sequence and an 18 bp His6 tag, with the 12 bp GGGS linker between them. The result is 216 bp, and the partition table reads 1-54, 67-186 and 199-216: each gap of 12 positions is the linker.
On By name the example loads three gene alignments for four taxa, withGallus gallus missing from the second gene. The result is 4 records of 63 columns, and the partitions are 1-24, 25-42 and 43-63. The Gallus record carries 18 gaps across gene 2, which is exactly how a supermatrix represents missing data.
Those three lines are the partition file for RAxML or IQ-TREE. To turn the output into PHYLIP or NEXUS, use thealignment format converter, and to strip gap-only columns first, the gap cleaner.
Paste them all into the box, or choose a FASTA file, and the In order tab joins them head to tail in the order they appear, as one record. Nothing is reordered and nothing is trimmed. The partition table under Details gives the first and last position of each part in the joined sequence.
A flexible glycine and serine linker is the usual choice for a fusion protein, most often (GGGGS) repeated one to three times, or the shorter GGGS in the list here. Keep the linker a multiple of three bases so the downstream domain stays in frame, and remove the stop codon from every part except the last one.
Paste the alignments one after another in a single FASTA and switch to the By name tab. Records are matched by the first word of the header, a new gene starts wherever a name repeats, and each taxon gets one record with all genes joined in order. A taxon missing from a gene is filled with gaps for the whole length of that gene, which is what a supermatrix expects.
Phylogenetics programs need to know where each gene starts and ends in the concatenated alignment so they can give it its own model. The partition lines under Details are in the format RAxML and IQ-TREE read, one line per gene, which you can paste straight into a partition file.
Yes. Type the record numbers in the Reverse complement field, for example 2 or 1, 3 or 2-4. Those records are reverse complemented before they are joined, which is how you fix a fragment that was sequenced or assembled on the other strand. The numbers are the positions in the input, counted from 1.