r maximum likelihoood tree - SERP Analysis

https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.html

https://www.molecularecologist.com/2016/02/26/quick-and-dirty-tree-building-in-r/

https://cran.r-project.org/web/packages/phangorn/vignettes/MLbyHand.html

https://rdrr.io/cran/ips/man/raxml.html

https://jhudatascience.org/AnVIL_Phylogenetic-Techniques/estimating-a-tree-using-maximum-likelihood.html

https://rpubs.com/mvillalobos/L01_Phylogeny

https://www2.decipher.codes/MaximumLikelihoodTrees.html

https://www.sciencedirect.com/topics/nursing-and-health-professions/maximum-likelihood-method

https://rdrr.io/github/geantonicelli/firstPackage/man/max_likelihood.html

https://www.reddit.com/r/bioinformatics/comments/secdpl/maximum_likelihood_with_mega/

https://pmc.ncbi.nlm.nih.gov/articles/PMC11117635/

https://iqtree.github.io/

https://github.com/mmatschiner/tutorials/blob/master/ml_phylogeny_inference/README.md

https://academic.oup.com/bioinformatics/article/21/4/456/203612

https://bioinformatics.stackexchange.com/questions/20115/maximum-likelihood-estimation-for-tree-construction

https://bioconductor.org/packages/devel/bioc/vignettes/DECIPHER/inst/doc/GrowingTrees.pdf

https://fuzzyatelin.github.io/bioanth-stats/module-24/module-24.html

https://www.reddit.com/r/evolution/comments/8249mi/please_explain_in_very_simple_laymans_terms_how/

https://www.researchgate.net/post/How-to-construct-phylogenetic-tree-with-maximum-likelihood-in-rstudio

https://bioinformatics.stackexchange.com/questions/13481/parsimony-and-maximum-likelihood-tree-comparison-in-r

https://pmc.ncbi.nlm.nih.gov/articles/PMC3035803/

https://community.appliedepi.org/t/how-can-i-generate-a-phylogenetic-tree-in-r-starting-from-a-fasta-file/221

https://www.rdocumentation.org/packages/phangorn/versions/2.12.1

https://www.youtube.com/watch?v=6SRS8vyvxcc

https://rug.mnhn.fr/semin-r/PDF/semin-R_phylogenetics_KSchliep_180310.pdf

https://www.molecularecologist.com/2017/02/08/phylogenetic-trees-in-r-using-ggtree/

https://epirhandbook.com/new_pages/phylogenetic_trees.html

https://yulab-smu.top/treedata-book/chapter1.html

https://en.wikipedia.org/wiki/List_of_phylogenetics_software

https://www.researchgate.net/post/Neighbor-joining-or-maximum-likelihood

https://klausvigo.r-universe.dev/phangorn

https://academic.oup.com/mbe/article/37/5/1530/5721363

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-538

http://iqtree.cibiv.univie.ac.at/

https://training.galaxyproject.org/training-material/topics/evolution/tutorials/abc_intro_phylo-mle-trees/slides-plain.html

https://cw.fel.cvut.cz/wiki/courses/bin/tutorials/tutorial6

https://www.nature.com/articles/s41467-020-20005-6

https://www.ihes.fr/~carbone/MaximumLikelihood2.pdf

https://bio.libretexts.org/Bookshelves/Evolutionary_Developmental_Biology/Phylogenetic_Comparative_Methods_(Harmon)/04%3A_Fitting_Brownian_Motion/4.03%3A_Estimating_rates_using_maximum_likelihood

https://www.analyticsvidhya.com/blog/2018/07/introductory-guide-maximum-likelihood-estimation-case-study-r/

https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12526

http://abacus.gene.ucl.ac.uk/ziheng/pdf/1993YangMBEv10p1396.pdf

https://learnplantscience.com/phylogenetic/r-for-phylogentic/

http://dunnlab.org/phylogenetic_biology/evaluation.html

https://www.megasoftware.net/web_help_10/Analysis_Options.htm

https://dl.acm.org/doi/abs/10.1145/1183907.1183909

https://www.jstor.org/stable/3070809

https://www.mimuw.edu.pl/~lukaskoz/teaching/sad2/books/Analysis_of_Phylogenetics_and_Evolution_with_R.pdf

https://link.springer.com/article/10.1007/BF01734359

https://github.com/venelin/PCMFit

https://en.wikipedia.org/wiki/Computational_phylogenetics

https://arftrhmn.net/creating-a-publication-quality-phylogeny-using-ggtree/

https://stackoverflow.com/questions/71058666/trying-to-root-a-phylogenetic-tree-using-phangorn-package-in-r

https://www.sciencedirect.com/science/article/pii/S105579032400160X

https://www.iqtree.org/doc/Complex-Models

https://yulab-smu.top/treedata-book/references.html

https://www.nature.com/articles/s41588-023-01368-0

https://www.pnas.org/doi/10.1073/pnas.95.21.12390

https://hal.science/hal-02535285/document

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-025-06080-w

https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=a31120d84eadf9b96dfb29a1307045b17b36fd77

https://www.mdpi.com/1424-2818/14/7/543

https://currents.plos.org/treeoflife/article/standard-maximum-likelihood-analyses-of-alignments-with-gaps-can-be-statistically-inconsistent/

https://bioinformaticsworkbook.org/phylogenetics/reconstructing-species-phylogenetic-tree-with-busco-genes-using-maximum-liklihood-method.html

https://research.rug.nl/files/1088003733/1-s2.0-S105579032400160X-main.pdf

https://faculty.nps.edu/ryoshida/pdf/Tokyo6.pdf

https://rannala.org/reprints/1997/Huelsenbeck1997a.pdf

http://www.phytools.org/***SanJuan2016/ex/2/Intro-to-phylogenies.html

https://www.reconlearn.org/post/practical-phylogenetics.html

https://www.rdocumentation.org/packages/ips/versions/0.0.11/topics/raxml

https://www.youtube.com/watch?v=6mOCtFR3N8w

https://itol.embl.de/

https://www.slideshare.net/slideshow/phylogenetics-cibio/32557351

https://www.geeksforgeeks.org/maximum-likelihood-estimation-in-r/

https://calla.rnet.missouri.edu/cheng_courses/slides9.pdf

https://www2.decipher.codes/MinimumEvolutionTrees.html

https://bdj.pensoft.net/article/10021/

https://help.geneious.com/hc/en-us/articles/360045071571-Which-maximum-likelihood-tree-builder-should-I-use

https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210x.12628

http://www.iqtree.org/doc/Dating

https://dmi.unibas.ch/fileadmin/user_upload/dmi/Studium/Computer_Science/Vorlesung_HS20/Lecture_Bioinformatics_Algorithms/Chapter04.pdf

https://www.biostars.org/p/16828/

https://link.springer.com/article/10.1007/BF02100082

https://stackoverflow.com/questions/63117891/r-code-for-maximum-likelihood-estimate-from-a-specific-likelihood-function

https://dl.acm.org/doi/10.1145/640075.640084

https://www.jstor.org/stable/2992355

http://dunnlab.org/phylogenetic_biology/phylogenies.html

http://www.ensembl.org/info/genome/compara/homology_method.html

https://www.youtube.com/watch?v=xKS5qZwl1GY

http://www.ipwgnet.org/cost/PDF%20files/Bioinformatics%20school/Bojan%20Duduk_r.pdf

https://figshare.com/articles/figure/_Maximum_Likelihood_tree_resulting_from_analysis_of_complete_mitochondrial_genomes_of_birds_with_an_emphasis_in_Rallidae_/1196791

https://xgboost.readthedocs.io/en/stable/parameter.html

https://www.geeksforgeeks.org/machine-learning/full-information-maximum-likelihood-for-missing-data-in-r/

https://www.youtube.com/watch?v=4WSrcwLm2B0

https://www.slideshare.net/slideshow/phylogenetics-in-r/10222772

https://www.sas.upenn.edu/~fdiebold/NoHesitations/BookAdvanced.pdf

https://www.youtube.com/watch?v=uAf0DCGynTk

https://www.youtube.com/watch?v=26SrCYRCQbY

https://scholarship.claremont.edu/cgi/viewcontent.cgi?article=1047&context=scripps_theses