A unified workflow for B-cell lineage reconstruction
Phylo Runner is a unified, reproducible framework for standardized B-cell lineage reconstruction across multiple phylogenetic methods. Run Dowser, GCtree, BrepPhylo and ClonalTree over one dataset through one workflow — every run recorded with its parameters and its random seed, so any result can be regenerated exactly.
Why use Phylo Runner?
The methods are powerful but hard to work with, and each expects its own inputs. Phylo Runner standardizes the way in, so the differences you see between methods come from the biology — not from your file format.
Standardized inputs, not edited files
Every method expects different column names. Map your dataset to each method's expected inputs once — the original file is never modified, and never re-uploaded.
Every run regenerates exactly
Parameters and the random seed are recorded with every run, so the same input yields the same tree — or carry the settings forward and change exactly one value.
Compare methods, not file formats
Trace the same sequence through four independent reconstructions and see where each method places it. The comparison is the point.
Analysis, not just display
Follow one sequence across four methods
Run the same clone through Dowser, GCtree, BrepPhylo and ClonalTree and each reconstruction places its sequences a little differently — a tip here, a deeper branch there. Sequence Trace pins one sequence and shows you exactly where every method puts it, side by side, so the disagreement between methods becomes something you can actually read.
Everything you get out of the box
Conveniences the raw command-line tools simply don't offer.
The raw tools have no user-friendly environment and are awkward to install and run. Phylo Runner wraps Dowser, GCtree, BrepPhylo and ClonalTree behind a single guided form.
Open the dashboardUpload TSV or CSV once and run all four methods — including GCtree, which natively accepts no tabular input — through behind-the-scenes conversion with no data loss.
Start a runEach method expects specific input column names. Map your columns to a method's expected inputs without editing your data and without re-uploading it.
Re-use the same uploaded dataset across as many runs as you like — there is no need to re-upload between runs.
Manage filesSend a previous run's settings into the next run and change a single value, instead of refilling the whole form by hand.
Open the dashboardWhen the same data is run multiple times, locate where a specific sequence sits in each run and compare the trees side by side.
Open Sequence TraceView each run's trees in multiple formats alongside the generated outputs. Results are saved and can be revisited; download images and the complete method output.
Browse run historyMethods execute server-side, so your local machine's resources aren't consumed while trees are built.
In every tree, click a node to see that node's complete information.
Supported methods