maximum-likelihood

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

bash r pipeline genomics perl phylogenetic-trees phylogenetics markers orthologues microbiology population-genetics codon-alignment maximum-likelihood phylogenomics species-trees recombination core-genome species-delimitation phylogenomics-pipeline clock-hypothesis

UpdatedJan 22, 2025
Perl

jkirkby3 /pymle

Star54

Maximum Likelihood estimation and Simulation for Stochastic Differential Equations (Diffusions)

python statistics simulation monte-carlo estimation fitting fit sde stochastic-differential-equations likelihood maximum-likelihood diffusion maximum-likelihood-estimation mle-estimation mle sdes brownian milstein ait-sahalia

UpdatedAug 6, 2025
Python

r-spatial /spatialreg

Star52

spatialreg: spatial models estimation and testing

bayesian impacts maximum-likelihood spatial-regression spatial-dependence spatial-econometrics

UpdatedSep 23, 2025
R

jabbring /dynamic-discrete-choice

Star49

Matlab package for learning to specify, compute, and estimate dynamic discrete choice models

matlab estimation exercises ddc maximum-likelihood mpec firm-dynamics dynamic-discrete-choice nested-fixed-point-method nfxp

UpdatedNov 22, 2023
MATLAB

grenaud /deML

Star48

Maximum likelihood demultiplexing

c-plus-plus sequencing maximum-likelihood demultiplexing

UpdatedFeb 14, 2025
C++

odubno /gauss-naive-bayes

Star45

Gauss Naive Bayes in Python From Scratch.

python naive-bayes naive-bayes-classifier bayesian bayes bayes-classifier naive-bayes-algorithm from-scratch maximum-likelihood bayes-classification maximum-likelihood-estimation iris-dataset posterior-probability gaussian-distribution normal-distribution classification-model naive-bayes-tutorial naive-bayes-implementation normal-naive-bayes naive-bayes-python

UpdatedMar 10, 2019
Python

pachadotdev /gravity

Sponsor

Star37

R package that provides estimation methods for Gravity Models

r gravity econometrics lm ols glm ddm trade maximum-likelihood nls tobit international-trade gpml ppml bvu bvw nbpml sils

UpdatedNov 21, 2024
R

evolbioinfo /pastml

Star37

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

visualisation phylogenetics phylogeography maximum-likelihood parsimony ancestral-character-reconstruction

UpdatedOct 23, 2025
Python

viodotcom /ppca_rs

Star36

Python+Rust implementation of the Probabilistic Principal Component Analysis model

python rust data-science machine-learning linear-algebra machine-learning-algorithms pca-analysis pca dimensionality-reduction missing-data maximum-likelihood em-algorithm maximum-likelihood-estimation missing-values

UpdatedAug 27, 2024
Rust

gokhanntosun /channel-estimation

Star35

Channel estimations based on RLS, LMS and ML methods.

estimation monte-carlo-simulation maximum-likelihood channel-estimation recursive-least-squares least-mean-squares

UpdatedJan 12, 2022
MATLAB

reslp /phylociraptor

Star27

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

bioinformatics snakemake pipeline genomics evolution phylogenetics reproducibility orthology-inference maximum-likelihood phylogenomics phylogenomics-pipeline species-tree

UpdatedAug 6, 2025
Python

vinuesa /TIB-filoinfo

Star26

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

bioinformatics tutorials linux-shell phylogenetics model-selection blast maximum-likelihood phylogenomics bioinformatics-scripts bash-scripting pangenomics multiple-sequence-alignment hmmer3 reciprocal-blast-hits profile-hmms

UpdatedOct 29, 2025
Shell

docnok /detection-estimation-learning

Star23

Python notebooks for my graduate class on Detection, Estimation, and Learning. Intended for in-class demonstration. Notebooks illustrate a variety of concepts, from hypothesis testing to estimation to image denoising to Kalman filtering. Feel free to use or modify for your instruction or self-study.

python machine-learning signal-processing detection jupyter-notebook regression estimation lasso ridge-regression hypothesis-testing maximum-likelihood teaching-materials kalman-filter python-notebook lasso-regression estimation-theory tikhonov-regularization

UpdatedApr 23, 2018
Jupyter Notebook

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maximum-likelihood

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CamDavidsonPilon /lifelines

3dem /relion

amkozlov /raxml-ng

Cibiv /IQ-TREE

stan-dev /cmdstanr

cogent3 /cogent3

jamiemcg /BUSCO_phylogenomics

vinuesa /get_phylomarkers