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seed initial clusters with premade shapes

Status: Open.

#58 In matsengrp/s2trajectory;

· chrisjenningsshaffer opened on Feb 13, 2025

duplicate entries for ORF1a

Status: Open.

#46 In matsengrp/s2trajectory;

· chrisjenningsshaffer opened on Oct 10, 2024

Consider a partially-joint neutral mutation model across mutation types

Status: Open.

#40 In matsengrp/s2trajectory;

· matsen opened on Jun 7, 2024

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NN-based neutral model

Regularization strategy

Status: Open.

#38 In matsengrp/s2trajectory;

· matsen opened on Jun 7, 2024

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NN-based neutral model

Address stochasticity in training

Status: Open.

#37 In matsengrp/s2trajectory;

· matsen opened on Jun 7, 2024

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NN-based neutral model

Format our output to look more like Jesse's

Status: Open.

#21 In matsengrp/s2trajectory;

· jgallowa07 opened on Sep 14, 2023

Break down ORF1a/ab into nps's

Status: Open.

#20 In matsengrp/s2trajectory;

· jgallowa07 opened on Sep 14, 2023

Filter MAT before chronumental

Status: Open.

#9 In matsengrp/s2trajectory;

· Haddox opened on Aug 29, 2023

Exclude sites that are prone to sequencing or base-calling errors

Status: Open.

#5 In matsengrp/s2trajectory;

· Haddox opened on Aug 9, 2023

Output number of nodes per subtree

Status: Open.

#4 In matsengrp/s2trajectory;

· Haddox opened on Aug 8, 2023

formalize generative model; simulate fitness trajectories and check inferences

Status: Open.

#3 In matsengrp/s2trajectory;

· matsen opened on Aug 7, 2023

node_1 has an inferred time of May 2019

Status: Open.

#2 In matsengrp/s2trajectory;

· Haddox opened on Aug 4, 2023