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.)

sequence_alignmentsequence_id

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).

Required must be presentOptional used if presentConditional needed for some options— not used

Column	Dowser	GCtree	BrepPhylo	ClonalTree
sequence_alignment	Required	Required	Required	Required
sequence_id	Required	Required	Optional	Required
clone_id	Required	—	Required	—
germline_alignment_d_mask	Required	—	Required	—
j_call	Required	—	—	Required
v_call	Required	—	—	Required
c_call Enable CSR / isotype analysis is enabled	—	—	Conditional	—
cdr1	—	—	—	Required
cdr1_end	—	—	—	Required
cdr1_start	—	—	—	Required
cdr2	—	—	—	Required
cdr2_end	—	—	—	Required
cdr2_start	—	—	—	Required
cdr3	—	—	—	Required
cdr3_aa	—	—	—	Required
cdr3_end	—	—	—	Required
cdr3_start	—	—	—	Required
cell_id Paired heavy/light (HL) chain mode	Conditional	—	—	—
d_call	—	—	—	Required
d_germline_alignment	—	—	—	Required
d_identity	—	—	—	Required
d_sequence_end	—	—	—	Required
d_sequence_start	—	—	—	Required
fwr1	—	—	—	Required
fwr2	—	—	—	Required
fwr3	—	—	—	Required
fwr4	—	—	—	Required
j_germline_alignment	—	—	—	Required
j_identity	—	—	—	Required
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
np2	—	—	—	Required
productive	—	—	—	Required
sequence	—	—	—	Required
v_germline_alignment	—	—	—	Required
v_identity	—	—	—	Required
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

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.

Download template (.tsv)TSV · required headers for all four methods · empty rows

Once uploaded, map each method's expected inputs on the run form, or read a specific method's field reference below.

Dowser GCtree BrepPhylo ClonalTree