Data requirements
Each method expects its own set of input columns. This page answers one question directly: which columns does your dataset need so you can run — and compare — every method on the same file? The tables below are generated from the same contracts the uploader validates against, so they never drift from what the app actually requires.
Universal columns
These columns are accepted by every method. A dataset that contains them can be run through all four and compared side by side. (Derived as the intersection of every method's accepted columns.)
Aligned sequence column · Sequence ID column
Full column matrix
Every column any method can use, and how each method treats it. Columns marked conditional are only needed when a particular option is enabled (noted inline).
| Column | Dowser | GCtree | BrepPhylo | ClonalTree |
|---|---|---|---|---|
sequence_alignment | Required | Required | Required | Required |
sequence_id | Required | Required | Optional | Required |
germline_alignment_d_mask Required when using the existing sequence_alignment; used as the germline root. | Required | — | Required | Conditional |
clone_id | Required | — | Required | — |
j_call | Required | — | — | Required |
v_call | Required | — | — | Required |
c_call Enable CSR / isotype analysis is enabled | — | — | Conditional | — |
cdr1 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr1_end Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr1_start Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr2 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr2_end Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr2_start Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr3 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr3_aa | — | — | — | Required |
cdr3_end Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cdr3_start Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
cell_id Paired heavy/light (HL) chain mode | Conditional | — | — | — |
d_call | — | — | — | Required |
d_germline_alignment Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
d_identity Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
d_sequence_end Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
d_sequence_start Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
fwr1 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
fwr2 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
fwr3 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
fwr4 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
j_germline_alignment Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
j_identity Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
j_region_end Region columns enabled (use_regions) | Conditional | — | — | — |
j_region_start Region columns enabled (use_regions) | Conditional | — | — | — |
j_sequence_alignment Refinement step enabled (on by default) | — | — | — | Conditional |
j_sequence_alignment_aa Refinement step enabled (on by default) | — | — | — | Conditional |
junction | Optional | — | — | — |
junction_aa | — | — | — | Required |
junction_length | Required | — | — | — |
locus Paired heavy/light (HL) chain mode | Conditional | — | — | — |
np1 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
np2 Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
productive | — | — | — | Required |
sequence Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
v_germline_alignment Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
v_identity Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
v_region_end Region columns enabled (use_regions) | Conditional | — | — | — |
v_region_start Region columns enabled (use_regions) | Conditional | — | — | — |
v_sequence_alignment Refinement step enabled (on by default) | — | — | — | Conditional |
v_sequence_alignment_aa Refinement step enabled (on by default) | — | — | — | Conditional |
v_sequence_start Required by alignment_intraclonal.py when ClonalTree builds per-clone trees. | — | — | — | Conditional |
File-format compatibility
Having the right columns is only half the story — the file must also be in a format the method accepts. To compare across methods, upload a format every target method accepts.
| Method | Accepted formats |
|---|---|
| Dowser | CSVTSVRDARDS |
| GCtree | FASTACSVTSVZIP |
| BrepPhylo | CSVTSV |
| ClonalTree | TSVCSV |
Sample dataset
A ready-to-fill template whose header row is every column the four methods require between them (in canonical AIRR names). Fill in your rows and the same file runs through all four methods with their default settings — no per-method reshaping.
Once uploaded, map each method's expected inputs on the run form, or read a specific method's field reference below.