Calendar · Lecture Notes
MIT OpenCourseWare
Computational Evolutionary Biology
Art: Palmer, Edward, 1803-1872, Figures 113-123. Plate Electrical Machines, 1840 · Public domain
- Instructor
- Prof. Robert Berwick
- Term
- Fall 2005
- Level
- Graduate
- What's inside
- 1 lecture note · 1 reading · 39 other files · 4 web pages
- Materials open
- MIT OCW
About this course
Source: MIT OpenCourseWare 6.877J Computational Evolutionary Biology, Fall 2005, Prof. Robert Berwick — original course page on ocw.mit.edu ↗. License: CC BY-NC-SA 4.0. Study order: MIT's own listing order, section by section. Taken from MIT's published course files, downloaded from ocw.mit.edu on September 23, 2026. How RedLectern is built.
Materials are grouped the way MIT organized them. A verified, course-wide order has not been established here.
Before you start
Prerequisites are not listed here. Check MIT's own syllabus for this course.
How this course was organized
What's here, and what isn't
- A lecture sequence of 23 items is confirmed. No assignments or exams were found for this course, so it stays as organized materials rather than a full course order.
Not included here
7 items from the source could not be safely included:
- MIT's page format for this item wasn't recognized clearly enough to place it safely. (7 items)
Materials by section
Grouped by section, as MIT organized them. Not sequenced or ordered.
Lecture Notes
- Introduction: The Basic Dynamical Systems of Evolution Download
- Evolution at the Molecular Level I Download
- Host-parasite Interactions and Disease Models Download
Labs
25 files
- Lab 1: Forces of Evolution · Part 1 Download
- Lab 1: Forces of Evolution · Part 2 Download
- Lab 2: Evolution, Polymorphism and the Coalescent · Part 1 Download
- Lab 2: Evolution, Polymorphism and the Coalescent · Part 2 Download
- This resource contains sequence data for question 5 for lab 2 part 1 (5sequencedata.txt) Download
- This resource contains a very simple awk script piS that computes the diversity statistic p and an… (PiSawk.txt) Download
- This resource contains sites drosophila data set for analyzing some real polymorphism data (sitestestdata.txt) Download
- This resource is a supporting file for lab 2 part 2, contains Macintosh version for installing and… (msmactar.gz) Download
- This resource is a supporting file for lab 2 part 2, contains compiled source code files (mslinuxtar.gz) Download
- This resource is a supporting file for lab 2 part 2, contains compiled source code files (mslinuxsourcetar.gz) Download
- This resource is a supporting file for lab 2 part 2, contains files for installing and running the… (msmacsourcetar.gz) Download
- This resource is a supporting file for lab 2 part 3, contains files for installing and running the… (mssource.zip) Download
- This is supporting file for lab 2 part 2 contains manual for running ms programs and generating… (msdoc.pdf) Download
- Lab 3: Detecting Selection · Part 1 Download
- Lab 3: Detecting Selection · Part 2 Download
- This resource is a supporting file for lab 3 part 1 containing sequence alignment of Plasmodium… (falciparum.fas) Download
- This resource is a supporting file for lab 3 part 1, contains codes (pf11_0344.fasta) Download
- This resource is a supporting file for lab 3 part 1, contains codes (Pfa3D7_chr11ORFs50.fasta) Download
- PAML Description Download
- This resource is a supporting file for lab 3 part 2 used with the PAML software (pamlexercise1.ctl) Download
- This resource is a supporting file for lab 3 part 2 contains codes run PAML software (codonmlpair.ctl) Download
- This resource is a supporting file for lab 3 part 2, contains codes (mhc.phy) Download
- This resource is a supporting file for lab 3 part 2 containing codes (codonmlsites.ctl) Download
- This resource is a supporting file for lab 3 part 2 which contains codes for the program run on… (codonmllineage.ctl) Download
- This resource is a supporting file for lab 3 part 2, contains PAML sequence file (paml_gstd1_seqfile.txt) Download
Other materials from this course
11 files
- This resource is a supporting reading file for lab2 part 2 which contains manual to run coalface… (coalface0_2b_mnl.pdf) Download
- This resource is a supporting file for lab 2 part 2, used for installing and running the CoalFace… (CoalFace03b.zip) Download
- This resource is a supporting file for lab 2 part 2, used installing and running the CoalFace… (CoalFace03btar.gz) Download
- This resource discusses the goal: understand this model, the "F=ma", a selectional model of… (lecture2.pdf) Download
- This resource discusses the interaction of evolutionary forces, II: mutationselection balance… (lecture4.pdf) Download
- This resource is a supporting file for lab 3 part 1, contains information on Plotkin's nature paper (plotkinnature04.pdf) Download
- plotkinnature2004.pdf Download
- This resource discusses the selectional model of evolution, Fisher?s proof of mud slides… (6877_lec2_1up.pdf) Download
- This resource contains Nei-Gojobori original papers which discusses the simple methods for… (nei_gojobori.pdf) Download
- This resource is a supporting file for lab 3 part 2, contains PAML documentation (pamldoc.pdf) Download
- This resource is a supporting file for lab 3 part 2, contains PAML faqs (pamlfaqs.pdf) Download
Course outline
Calendar · Lecture Notes
Lecture 2: Forces of Evolution I: Complications
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Lecture 3: Forces of Evolution II: Optimization
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Lecture 4: Forces of Evolution III: Mutation, Migration
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Lecture 5: Forces of Evolution IV: Genetic Drift
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Lecture 6: Evolution at The Molecular Level I
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Lecture 7: Evolution at The Molecular Level II
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Lecture 8: Evolution at The Molecular Level III
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Lecture 9: The Algebra of Evolution: Price’s Theorem I
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Lecture 10: The Algebra of Evolution: Price’s Theorem II
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Lecture 11: Detecting Selection
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Lecture 12: Detecting Selection: A Case Study
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Lecture 13: Codon Volatility
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Lecture 14: Coalescent Theory and Phylogenetics
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Lecture 15: Evolutionary Phylogenetics
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Lecture 16: Evolutionary Phylogenetics (cont.)
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Lecture 17: Quantitative Genetics I
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Lecture 18: Quantitative Genetics II Host-parasite Interactions
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Lecture 19: Host-parasite Interactions and Disease Models
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Lecture 20: Evolutionary Stable Strategies
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Lecture 21: Developmental Evolution
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Lecture 22: Quantitative Genetics II
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Lecture 26: Finale: The Future of Evolution
MIT OpenCourseWare, Prof. Robert Berwick, 6.877J Computational Evolutionary Biology, Fall 2005.
License: CC BY-NC-SA 4.0 · Edition: Fall 2005 · Open the original course on OCW ↗
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