Multiz Alignments of 7 Yeasts
 

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Alignment block 1 of 3 in window, 498853 - 499292, 440 bps 
B D  S. cerevisiae  caatcaacgatggtgctgcagccgtcatcttggtttccgaaaaagttttgaaggaaaagaatttgaagcc
            sacPar  caatcaacgatggtgctgcagctgttattttggtttctgaaaaaattctaaaggaaaagaatttgaagcc
            sacMik  caattaacgatggtgctgcagctgtcattttggtttctgaaaaagtcttgaaggaaaaaaatttgaaacc
            sacKud  caatcaacgatggtgccgcagctgtcattttggtgtctgaaaagatcttaaaggaaaagaatttgaaacc
            sacBay  caatcaacgacggtgccgcagctatcattttagtctctgaaagagtcttgaaggaaaagaatctaaaacc
            sacCas  caattaacgatggtgctgctgcagtcattctagtatctgaaagaaagttacaagagttgaagttgacacc
            sacKlu  caattaacgatggtggtgccgccgtggtcttggtttctgaacgcaagttgagggaattgaatttgactcc

     S. cerevisiae  tttggctattatcaaaggttggggtgaggccgctcatcaaccagctgattttacatgggctccatctctt
            sacPar  tttagctatcgtcaagggttggggtgaggccgctcatcaaccagctgacttcacatgggctccatctctt
            sacMik  tttagccattgttaagggctggggtgaggccgctcatcaaccagctgacttcacatgggctccatccctt
            sacKud  tctagctattatcaagggttggggtgaagctgctcaccaaccggctgatttcacatgggctccatctctt
            sacBay  cttggctctcatcaaaggttggggtgaagcagcccatttaccagctgatttcacatgggccccatccctt
            sacCas  cttggctgtcattaggggttggggtgaagccgctcaacatcctgctgattttacatggtctccttcatta
            sacKlu  cctagcaattattaagggctggggtgaagctgctcacgaacctgcagactttacgtgggcaccttctttg

     S. cerevisiae  gcagttccaaaggctttgaaacatgctggcatcgaagacatcaattctgttgattactttgaattcaatg
            sacPar  gcagttccaaaggctttgaaacatgccggcatcgaagatattagttccgttgattactttgaattcaatg
            sacMik  gcagttccaaaggcattgaaacatgccggtatcaaagatattaacgccgttgattactttgaatttaacg
            sacKud  gctgttccaaaggctttgaaacatgctggtatcgaagatatcagctccgtagactactttgagtttaacg
            sacBay  gcagttccaaaggctttgaaacatgctggtatcgaagatatcaattccgtagactacttcgaattcaacg
            sacCas  gctgttccaaaggcattaaagcatgcaggtatttccgatatacaatccgttgatttctttgaatttaatg
            sacKlu  gccattccaaaggccttgaaacatgcaggcgtggaggacatcaaccaggtcgacttttttgaactaaacg

     S. cerevisiae  aagccttttcggttgtcggtttggtgaacactaagattttgaagctagacccatctaaggttaatgtata
            sacPar  aagctttttcagtcgtcggtttggtcaacaccaagattttgaagctagacccatctaaggttaatgtata
            sacMik  aagctttttctgtcgtcggtttggttaacactaagattctgaagctagacccttctaaggttaatgtgta
            sacKud  aagccttttccgtggtcggcctggtcaacactaagatcttgaagctagatccatcgaaggttaatgtata
            sacBay  aagctttctccgtcgttggtttggttaacactaagattctaaagctagacccatctaaggttaatgtata
            sacCas  aggctttctccgttgtaggaattgctaatacaaagattctaaagttaaatccagctaaagttaatgttta
            sacKlu  aggctttctcagttgttggtttggcaaacaccaaaatcctaaacattgctccagaaaaggtcaacgtcta

     S. cerevisiae  tggtggtgctgttgctctaggtcacccattgggttgttctggtgctagagtggttgttacactgctatcc
            sacPar  cggtggcgctgttgctttaggccatccattgggttgttcaggtgccagagtggtcgttactctactatcc
            sacMik  cggtggtgccgttgccttaggtcatccattgggttgttctggtgccagagtggttgttacactgctatcc
            sacKud  cggtggtgctgttgccttagggcatccattgggttgctctggtgccagagtggtcgttactctgctatcc
            sacBay  cggtggtgcagtcgctttaggacatccattgggttgttcaggtgccagagtggtcgttactctactatct
            sacCas  tggtggtgcagttgccattggtcatcctcttggttgttcaggtgctagaattgtagttactttgctatct
            sacKlu  cggtggtgctgttgccattggtcacccattgggttgctccggtgccagaattattgtcactttagccact

     S. cerevisiae  atcttacagcaagaaggaggtaagatcggtgttgccgccatttgtaatggtggtggtggtgcttcctcta
            sacPar  attttacaacaagagggaggtaagatcggtgttgccgccatctgcaatggtggtggtggtgcttcatcta
            sacMik  attttacaacaagagggaggtaagatcggtgttgctgctatctgtaatggtggtggtggtgcttcatcta
            sacKud  attctacaacaagaaggaggtaagatcggtgttgctgccatctgtaatggtggcggtggtgcttcatcca
            sacBay  attctacagcaagagggaggtaagatcggtgttgctgccatctgtaatggtggtggtggtgcttcttcta
            sacCas  atattacgtcaagaaaagggtaagcttggtgttgctgctatctgtaatggtggtggtggtgcctcttcca
            sacKlu  gtcttacaacaagaaggtggtaaactaggtgtcgctggtatctgtaatggcggtggtggtgcatcctcca

     S. cerevisiae  ttgtcattgaaaagatat--ga
            sacPar  ttgtcattgaaaagatat--ga
            sacMik  ttgtcattgaaaagatat--ga
            sacKud  tcgtcattgaaaagatat--ga
            sacBay  tcgtcattgaaaagctat--ga
            sacCas  ttgtcattgaaagactatagga
            sacKlu  tcgttttggaaagggttt--ga

Alignment block 2 of 3 in window, 499293 - 499374, 82 bps 
B D  S. cerevisiae  ttacgttct-gcgattttctcatga----------tctttttcataaa---------atacataaatata
            sacPar  ttgcgtttc-gcga-tttctcataa----------tc-tttccataaa---------atacataaatata
            sacMik  ttaaattcctgttg-tttttcataa----------tc-ttttttt--a---------atacataaatata
            sacKud  tcgcattct-aag--ttttccataa----------tc-ttctc-taaa---------acacataaatata
            sacBay  ttgcatttt-gtg--ttttttatca----------tc-ttttcctaaatccataaatatatatatatata
            sacCas  aggaggttt-gctt-ttgtgcataaggttagctattc-attgtataaa---------ttaattaattata

     S. cerevisiae  t-------------aaatggctttatgtataacaggcataattta
            sacPar  t-------------aaatggctttatgtataacaagcataattta
            sacMik  t-------------aagtggctttatgtataataagcataattt-
            sacKud  t-------------aaatggctttatatataacaagcataattta
            sacBay  t-------------ataaagcttcatatataacaagcataattta
            sacCas  ttgaaataacaaaagaatgatttcaagtaaaaaaggaataaatta

Alignment block 3 of 3 in window, 499375 - 500557, 1183 bps 
B D  S. cerevisiae  aagttttatttgcgattcatcgtttt------tcaggtactcaaacgctgagg------tgtgccttttg
            sacPar  aagttttatttgcaaatcttttcttt------tacagtatttgaacggcaaaa-------atgcctttcg
            sacMik  aagttctatttccaattcttttctttacggcggcaggtattcataaactaaagtata-ctatgccatata
            sacKud  aagttttatttgcag--------ttt------tgaggtattcg-atagcgatgtacgtttttgccttatg
            sacBay  aatttttatttgcaattc-----ctt------aacgttattta-ttaaaaggg-------ctacctttta

     S. cerevisiae  acttacttt-tccgccttggcaagctggccgggtgat----acttgcacaagt----tc-cactaattac
            sacPar  agccattttctccgccttagcaggcaggccgggtgat----aattgcacaagc----tt-cactaattac
            sacMik  cttggtttt-tccgcttgggtaaattggccgggtgatg---aacccttcaaat----tcgtgttaattac
            sacKud  atttgtttt-ttcgcctttgcgaataggccgggtgat----gatcgtaccagt----tc-aattaattac
            sacBay  ctcggtttt-tctgccttcgcgc-tgagccgggtcatacataattgtacaagtctaatt-agttaattac

     S. cerevisiae  tgacatttgtggtattaactcgtttgactgct-ctacaattgtaggatgttaatcaatgtc--ttggctg
            sacPar  tgacatttgtggtatc-acgcggttgatccat-ctacaattgtaggacactaatcaaggtcaaattgccg
            sacMik  tgacatttgtggtata-agcagtttgattcctgctacaattgtagaaggctgagcaag-----tttgaac
            sacKud  tgacatttgtggtatc-aggtgttcgaccttt-ttgcaactgtagaactctgaccaagct---ctggctg
            sacBay  tgacgtttgtggttt--gggtactcgat--at-tcaccattgtgtgcagcttatctggcgctaactgatt

     S. cerevisiae  ccttcatt-ctcttcaggctctatt----------aattttaa-ccgtt------------ataagttcc
            sacPar  ttctcat---tcttcattttcaatt----------tatataaagtcgtt------------tcaagttca
            sacMik  ttttcttt--actttaaattttgtc----------aattaaaa-acgtt-------------caaattct
            sacKud  tattt-----tcactaggtcctatttcttcttcgcaattgaaa-tcaat------------ttaagttct
            sacBay  tttacactgggtattgtttttggtt----------aactgaaa-ctactctctaaatgcagctatttttc

     S. cerevisiae  t-------------------tttctcccttgg--------aagcaaaca--------tcaactgcctta-
            sacPar  t-------------------tttatcccttg----------agcaagca--------ttaactgcctca-
            sacMik  t-------------------ttcatctcttgg--------aaacaaacatttggt-tttaagtatcgca-
            sacKud  tttggagcctagtttttttctttttctctt---------------------------atagctatctgaa
            sacBay  t-------------------tttttcttttggtaattcgaaagcaagcattccgtgcctatttgactta-

     S. cerevisiae  ---aaatctggtggcgagga-aagaggaaatggcatgtactaatgatggtcctaataaatatcccgaaat
            sacPar  ---aaatttggttgtgagaagaagagaaaatgacatgcacgaatggtgatcctgataaacatctcgaaat
            sacMik  ---aagtgtggttgaaaaaa-tagggaaaatgacaggcaacagtgaagatgctgggaaacatctcgaaaa
            sacKud  agcaaacgtggttgagaaaa-------aaatggcatgcgttgaaggtgatcctaataaatctcttgaaaa
            sacBay  ---aagcctggttg----aa-------aaatgccatgcgatcctgctactccagacaatcctctcaacaa

     S. cerevisiae  tgtgagtgttaagcacctgttccaacattcgggatccaagcatgaatttagtgctggtaaacgattttca
            sacPar  ggtgagtgtaaagcatttgttccagaattcgatatccaggcatgaatctagcgctggtaaacgattttca
            sacMik  ggtgagcgtcgagcaccttttccaagattcgagattcaagcatgaaactcatcttcacaaacaattttca
            sacKud  ggtcagcataaagtgtctcttccaggattcgaggttcaagcaggactctaatccccatagaaggtttgta
            sacBay  ggtgagtgtaaaagagctcttccaaaatgcgagacttgagaaaactccaaatttcaataaacgatttgtt

     S. cerevisiae  aaatccattggtaaaatattcaaacgaaactctgctttgaaaacttctagaactgaaacggcaaatcata
            sacPar  aaatcccttggtagattcttcaagcagaatgctgtttcgaaaactcatagaactgaaacgggaaatcaca
            sacMik  gagacccttggtaaaatttttcagcaaaaaattgttattaaaactcatagaactgatgctgaatatcacc
            sacKud  agattcctgggaaagatctttaagcga---tctgttacg------------actgaaacgggaaaccaca
            sacBay  gaacccctttggaagatctttaagcggcctgtggtttcaaaacctcatacaacgaggacatcaagccaca

     S. cerevisiae  aaatggaattgaaaaaaagagagggtgttaccttattgccacctgtcccagaatcattattacataaact
            sacPar  acatagagttgaaaaaaaaagatggcgttactttactgcctcctgtctccgaatcattattacataaagt
            sacMik  atagagagttgagagaaaaggagggtgttactttattaccacctgttccggaatcgttattacataaagc
            sacKud  gcagggagttgaaaaagaaagagggcgtaaccttgctgccacccgtcccagagtcattattacataaact
            sacBay  gtaaggagctgagaaaaaaggaaggcgtcactttactgccacctgtcccggaatcattattccatagatt

     S. cerevisiae  caattcttggttggaaac---tttttcttccaccaagaacatga------------aaatcgaagaaaac
            sacPar  caattattggctcgaaacttttttttctcccgctaagaagatgc------------aaatcgaagaaaat
            sacMik  caactttttgctcgaagctttttgctcttctgataagagaatgccaaaggaatatgaaatggaagaaaac
            sacKud  tagattcaggctcgagtctttttactttcccattaaaaaagcgcaaaaagaatcagaaatcgaagagtcc
            sacBay  taatttctggctcaaggctctttactgtcccattggcaggaaacaagaagcagacgagacgaaagatacc

     S. cerevisiae  aaaattgttattaatgaaaaagagattcgggattcagtctcttactaccctgataagaatggaggaagtg
            sacPar  aagatcgttattaatgaaaaagagattcgagattcggtttcttactatcctgataagaatggaggaagtg
            sacMik  aaaattgtagttaatgaaaaagacattcgagattcggtttcttactatcctgataagaacggaggaagtg
            sacKud  aaaatcgtaatcaatgaaaagcaggttcgggattcagtctcctgttttcctgatgagaatggaggaagtg
            sacBay  aaaatcgttattaatgaaaaacagatccgggattcaatttcgttttatccagacgaagaaaaagggagtg

     S. cerevisiae  ctgtattttgttacttgcccgaccttgtgctatattataagccgcctataaaagtcacaggcaagcaatg
            sacPar  ttgtgttttgttgcttgcccgaccttgtgttatattataagccgccaataaaagtaacaggcaagcaatg
            sacMik  ttgtgttttgttacttgccagatcttgtgttgtattttaaaccgccaatgaaagtgacaggaaaacaatg
            sacKud  ttgtgttctgttatctgcccgaccttgtgttgtactataggccaccagtgaaagtgacaggaaggtcatg
            sacBay  ttgtgttttgctacctacctgacctagtattgtattacacaccgccgatgaaagtgactggaaagccatg

     S. cerevisiae  tccaataaagagaagtccttgggaatcgatggaaatccaatatcaaaagtttatgtaccccttagaaagg
            sacPar  tccaataaagagaagtccttgggaatcgatggagatccaatatcaaaagtttatgtatcccttggaaagg
            sacMik  tccaataaagagaagtccttgggaattgatggagatccagtatcaaaagtttatgtatcccttagaaaaa
            sacKud  ccctataaagagaagcccctgggactcgatggagatccaatatcaaaagtttatgcaccccttggaaagg
            sacBay  tcctataaagaaaagcccctgggaatcgatggagatccgataccaaaagttcatgtatccgttggaaaaa

     S. cerevisiae  ttggaaagacagtttgaggaagttccatttaggccctggtattttgcaatgcgattaaaggaactttaca
            sacPar  ctagagagacagtttgaggaagttccttttaggccctggtatttcgcaatgcgattaaaggaactttata
            sacMik  ctagaaagacaatttgaggaagttccttttagaccctggtacttcgcaatgcggctaaaggaactctata
            sacKud  ttagaaaaacaatttgaagaagttccctttaggccctggtatttcgctatgcggttgaaggaactttata
            sacBay  ttagaaggacaatttgaggaagtcccctttagaccctggtttttcgctatgcgcttgaaagagctctata

     S. cerevisiae  gatgctgtgaaaggtcttttactaacgcggcaaatagaggaaaggcaaggttattgcgggggaagcaaag
            sacPar  gatgctgtgaaaggtcttttactaacgcggcaaatagaggtaaggcaaggttattgcgcgggaagcaaag
            sacMik  gatgctgtgaaaggtcttttactaacgcggcaaatagaggtaaggcaaggctattgcgtggaaagcaaag
            sacKud  ggtgctgtgaaaggtccttaactaacgcggcaaatagaggtaaaacaaggttattgcgggggaaacagag
            sacBay  gatgcttggaaaggtcttttagtaatgcggcaaatagaggtaaggcaaagctgctgcgagggaaacaaag

     S. cerevisiae  gacgaaaaaatcgtatcataagactgtcaacctggtatcagcgaagatttccacccattcaaatgcgccg
            sacPar  aacgaaaaaatcgtatcatgaaactgtcaacttagtctcaatgaagatttgcacttatccaaatgcacca
            sacMik  aacaaaaaagtcgtaccatagaactgtcgatttagtgtcaatgaagatttctgcgcattcgaatgcgtca
            sacKud  aacaaaaaaatcgtaccataaaactgtcaatttagtctctatgaagatttccacccattcaaatgcgtca
            sacBay  aacaaagaaatcgtatcacaaaaccgttaatttggtgtcgatgaagatttccacccatcaacat------

     S. cerevisiae  tcgccgggctga-gaaacaaaaaaagtgactaagttctgtcattctatcattattgtaatt-agttatgt
            sacPar  tcacctcggtga-gaaactaaaaaagtggctaaatt-tgtcattctatcattattgtaatt-agttatgt
            sacMik  tcgccttactgatgaaaaaaaacaataaactaagtt-tgcaattctatcattattataattaagttgtgt
            sacKud  tcgcaccgctga-aagttaaaagaaaaa---------tgtcattctatcattattataattaagttatgt
            sacBay  ---tcccgctaa-aacat-------------------taccattctatcattattataattaggttatgt

     S. cerevisiae  aggac--------atatatatccatagtg--atctccttttgatc-aaagaagacactgaaaagtcgtaa
            sacPar  aggac--------atatatatccgtatag--atctccttttgatcaaaagaagacattgaaaagtcgtaa
            sacMik  aggacgtatatgtgtatatatccgcggtg--atcttctttggatcaaaagaagacattgaaaagtcgtaa
            sacKud  aggacgtatat--atatatatccgttttgtaatcttccttccggtgtaagagaagtagaaaaagtcgtaa
            sacBay  aggacgtatatatataaatattcgtatta--atcttctctagatt-aaaaaaaagttgaaaaagtcataa

     S. cerevisiae  gttcgtaaaaaaagtatgaaaatcgttccagccattgctt
            sacPar  gttcgtaaaaaaagtatgaaaattattccagccagcgctt
            sacMik  gttcgtgaaaaaagtataaagatccctccag----tgctt
            sacKud  gttcgtgaaaaaaatatggaaattttttc---ctgtgctt
            sacBay  gttcgtgaaaa---tacagaaagc-ctccag----tgctt

View table schema

Go to Conservation track controls

Data last updated at UCSC: 2011-09-01

Description

This track shows a measure of evolutionary conservation in seven species of the genus Saccharomyces based on a phylogenetic hidden Markov model (phastCons). The graphic display shows the alignment projected onto S. cerevisiae.

The genomes were downloaded from:

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the S. cerevisiae genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 bases or fewer, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the S. cerevisiae genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Downloads for data in this track are available:

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the S. cerevisiae sequence at those alignment positions relative to the longest non-S. cerevisiae sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene TrackSpecies
SGD GenesS. cerevisae
No annotationall the other yeast strains
Table 2. Gene tracks used for codon translation.

Methods

Best-in-genome pairwise alignments were generated for each species using lastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, and the resulting multiple alignments were assigned conservation scores by phastCons.

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

Credits

This track was created at UCSC using the following programs:

  • Lastz (formerly Blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group.
  • AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC.
  • PhastCons by Adam Siepel at Cornell University.
  • "Wiggle track" plotting software by Hiram Clawson at UCSC.

The phylogenetic tree is based on the Saccharomyces Phylogeny page from the Department of Genetics at Washington University in St. Louis.

References

Phylo-HMMs and phastCons:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.