534:
309:
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305:. In principle, since there are four base types, with 1000 base pairs, we could have 4 distinct haplotypes. However, for organisms within a particular species or in a group of related species, it has been found empirically that only a minority of sites show any variation at all, and most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is relatively small.
2296:
1676:
510:). The fourth stage consists of various methods of tree building, including distance-based and character-based methods. The normalized Hamming distance and the Jukes-Cantor correction formulas provide the degree of divergence and the probability that a nucleotide changes to another, respectively. Common tree-building methods include unweighted pair group method using arithmetic mean (
501:
Another molecular phylogenetic analysis technique has been described by
Pevsner and shall be summarized in the sentences to follow (Pevsner, 2015). A phylogenetic analysis typically consists of five major steps. The first stage comprises sequence acquisition. The following step consists of performing
168:
correlate. Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and
288:
in either DNA or RNA segments extracted using different techniques. In general, these are considered superior for evolutionary studies, since the actions of evolution are ultimately reflected in the genetic sequences. At present, it is still a long and expensive process to sequence the entire DNA of
593:
sampling problems must be addressed. This means that strikingly different results can be obtained by applying different models to the same dataset. The tree-building method also brings with it specific assumptions about tree topology, evolution speeds, and sampling. The simplistic UPGMA assumes a
549:
is an approach that is commonly used to measure the robustness of topology in a phylogenetic tree, which demonstrates the percentage each clade is supported after numerous replicates. In general, a value greater than 70% is considered significant. The flow chart displayed on the right visually
140:
that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular
329:
is used; however, many current studies are based on single individuals. Haplotypes of individuals of closely related, yet different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: these are referred to as an
544:
is an analysis software that is user-friendly and free to download and use. This software is capable of analyzing both distance-based and character-based tree methodologies. MEGA also contains several options one may choose to utilize, such as heuristic approaches and bootstrapping.
530:, which are character-based/model-based methods. UPGMA is a simple method; however, it is less accurate than the neighbor-joining approach. Finally, the last step comprises evaluating the trees. This assessment of accuracy is composed of consistency, efficiency, and robustness.
376:
is examined in order to see whether the samples cluster in the way that would be expected from current ideas about the taxonomy of the group. Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a
1059:
Cabra-García, Jimmy; Hormiga, Gustavo (2020). "Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: A case study with the
Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)".
361:. The advantage claimed for using hybridization rather than gene sequencing was that it was based on the entire genotype, rather than on particular sections of DNA. Modern sequence comparison techniques overcome this objection by the use of multiple sequences.
421:
of these substances, while the molecules of organisms distantly related often show a pattern of dissimilarity. Conserved sequences, such as mitochondrial DNA, are expected to accumulate mutations over time, and assuming a constant rate of mutation, provide a
2139:
573:
among organisms provides a significant complication to molecular systematics, indicating that different genes within the same organism can have different phylogenies. HGTs can be detected and excluded using a number of phylogenetic methods (see
502:
a multiple sequence alignment, which is the fundamental basis of constructing a phylogenetic tree. The third stage includes different models of DNA and amino acid substitution. Several models of substitution exist. A few examples include
493:
There are several methods available for performing a molecular phylogenetic analysis. One method, including a comprehensive step-by-step protocol on constructing a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly,
334:. The base sequences for the haplotypes are then compared. In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of
312:
In a phylogenetic tree, numerous groupings (clades) exist. A clade may be defined as a group of organisms having a common ancestor throughout evolution. This figure illustrates how a clade in a phylogenetic tree may be
243:
began around 1956. Although the results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of
350:, by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA that is sequenced.
301:. At any location within such a sequence, the bases found in a given position may vary between organisms. The particular sequence found in a given organism is referred to as its
2084:
2048:
1987:
498:, model-test (testing best-fitting substitution models), and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol.
1882:
2066:
581:
In addition, molecular phylogenies are sensitive to the assumptions and models that go into making them. Firstly, sequences must be aligned; then, issues such as
566:. This is a limitation when attempting to determine the optimal tree(s), which often involves bisecting and reconnecting portions of the phylogenetic tree(s).
469:. Another application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever-more-popular use of
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443:
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Philippe, H.; Brinkmann, H.; Lavrov, D. V.; Littlewood, D. T. J.; Manuel, M.; Wörheide, G.; Baurain, D. (2011). Penny, David (ed.).
1714:
1279:
2115:
1892:
791:
Suárez-Díaz, Edna & Anaya-Muñoz, Victor H. (2008). "History, objectivity, and the construction of molecular phylogenies".
2072:
1970:
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17:
906:
Sanger F, Coulson AR (May 1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase".
1828:
1474:
550:
demonstrates the order of the five stages of
Pevsner's molecular phylogenetic analysis technique that have been described.
2098:
1002:"Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction"
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2004:
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approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be
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1782:
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for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable
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in one haplotype that is not present in another). The difference between organisms is usually re-expressed as a
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help in providing reliability estimates for the positions of haplotypes within the evolutionary trees.
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1981:
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International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
2010:
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293:). However, it is quite feasible to determine the sequence of a defined area of a particular
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Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences
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In a molecular systematic analysis, the haplotypes are determined for a defined area of
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Microsoft
Research - University of Trento Centre for Computational and Systems Biology
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461:, wherein the species of an individual organism is identified using small sections of
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Once the divergences between all pairs of samples have been determined, the resulting
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1143:"Molecular systematics: a synthesis of the common methods and the state of knowledge"
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506:, the Jukes and Cantor one-parameter model, and the Kimura two-parameter model (see
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techniques to identify similarity. Another application of molecular phylogeny is in
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in 1977, it became possible to isolate and identify these molecular structures.
417:. In general, closely related organisms have a high degree of similarity in the
338:(other kinds of differences between haplotypes can also occur, for example, the
1723:
1539:
1089:"Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough"
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An older and superseded approach was to determine the divergences between the
297:. Typical molecular systematic analyses require the sequencing of around 1000
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rooted tree and a uniform molecular clock, both of which can be incorrect.
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Branch of phylogeny that analyzes genetic, hereditary molecular differences
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248:, for example, needed substantial revision. In the period of 1974–1986,
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Inferring horizontal gene transfer § Explicit phylogenetic methods
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Pevsner, J. (2015). "Chapter 7: Molecular
Phylogeny and Evolution".
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inference of phylogenetic relationships using transcriptomic data
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153:, a broader term that also includes the use of molecular data in
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1914:
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was the dominant technique used to measure genetic difference.
828:"Charles G. Sibley: A commentary on 30 years of collaboration"
66:
1946:
1872:
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1397:
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511:
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African
Society for Bioinformatics and Computational Biology
1988:
Max Planck
Institute of Molecular Cell Biology and Genetics
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208:
128:
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89:
83:
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51:
42:
650:(2003) , Peter Roach; James Hartmann; Jane Setter (eds.),
203:. Applications of molecular systematics were pioneered by
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86:
60:
410:
406:
260:
Early attempts at molecular systematics were also termed
104:
57:
2067:
International
Nucleotide Sequence Database Collaboration
749:. Kluwer Academic Publishers Boston, Dordrecht, London.
368:
of differences is submitted to some form of statistical
477:, as well as the emergence of a new branch of criminal
276:. These have been replaced in recent times largely by
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110:
107:
95:
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71:
54:
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321:; a substantial sample of individuals of the target
169:
results in the construction of a phylogenetic tree.
101:
80:
63:
48:
1058:
1038:(3rd ed.). Wiley-Blackwell. pp. 245–295.
745:Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1998)
125:
116:
92:
45:
39:
1759:, database of protein sequences grouping together
943:"DNA sequencing with chain-terminating inhibitors"
871:Molecular evolution : a phylogenetic approach
747:Molecular Systematics of Plants II: DNA Sequencing
488:
941:Sanger F, Nicklen S, Coulson AR (December 1977).
2314:
1994:US National Center for Biotechnology Information
825:
2079:International Society for Computational Biology
542:MEGA (molecular evolutionary genetics analysis)
2146:ISCB Africa ASBCB Conference on Bioinformatics
1236:NCBI – Systematics and Molecular Phylogenetics
537:Five Stages of Molecular Phylogenetic Analysis
449:The most common approach is the comparison of
396:
2093:Institute of Genomics and Integrative Biology
1708:
1273:
905:
2122:European Conference on Computational Biology
1080:
430:of various organisms. With the invention of
2157:Research in Computational Molecular Biology
773:. 2nd ed. Sinauer Associates Incorporated.
149:. Molecular phylogenetics is one aspect of
2134:International Conference on Bioinformatics
1715:
1701:
1280:
1266:
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1025:
934:
864:
2128:Intelligent Systems for Molecular Biology
1211:
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1104:
1062:Zoological Journal of the Linnean Society
1013:
976:
966:
793:Stud. Hist. Phil. Biol. & Biomed. Sci
654:, Cambridge: Cambridge University Press,
522:, which is a character-based method, and
255:
183:The theoretical frameworks for molecular
1147:Cellular & Molecular Biology Letters
899:
558:Molecular systematics is an essentially
532:
307:
280:, which produces the exact sequences of
239:(who studied various groups). Work with
2116:Basel Computational Biology Conference
1185:
1033:
1022:
634:
187:were laid in the 1960s in the works of
14:
2315:
1036:Bioinformatics and Functional Genomics
2073:International Society for Biocuration
1971:European Molecular Biology Laboratory
1696:
1261:
646:
2295:
1675:
1141:San Mauro, D.; Agorreta, A. (2010).
999:
993:
518:, which are distance-based methods,
2099:Japanese Society for Bioinformatics
700:. Sinauer Associates Incorporated.
24:
2061:European Molecular Biology network
1722:
1134:
569:The recent discovery of extensive
25:
2339:
2151:Pacific Symposium on Biocomputing
2055:Australia Bioinformatics Resource
2022:Swiss Institute of Bioinformatics
2005:Netherlands Bioinformatics Centre
1965:European Bioinformatics Institute
1287:
1229:
2294:
2283:
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1953:Database Center for Life Science
1941:Computational Biology Department
1829:Arabidopsis Information Resource
1674:
1663:
1662:
1515:Phylogenetic comparative methods
1339:
728:. Chapman & Hall, New York.
405:contains deoxyribonucleic acid (
35:
1799:Specialised genomic databases:
1520:Phylogenetic niche conservatism
1188:"The promise of a DNA taxonomy"
1052:
726:Molecular systematics of plants
489:Molecular phylogenetic analysis
438:may also be used to obtain the
2000:Japanese Institute of Genetics
858:
819:
784:
760:
739:
711:
687:
680:Merriam-Webster.com Dictionary
667:
652:English Pronouncing Dictionary
640:
553:
179:History of molecular evolution
13:
1:
1920:Rosalind (education platform)
1837:Zebrafish Information Network
1805:Saccharomyces Genome Database
524:Maximum likelihood estimation
481:focused on evidence known as
2250:List of biological databases
1769:Protein Information Resource
1106:10.1371/journal.pbio.1000602
947:Proc. Natl. Acad. Sci. U.S.A
920:10.1016/0022-2836(75)90213-2
164:Molecular phylogenetics and
7:
1743:European Nucleotide Archive
1440:Phylogenetic reconciliation
1347:Evolutionary biology portal
1303:Computational phylogenetics
805:10.1016/j.shpsc.2008.09.002
604:Computational phylogenetics
597:
496:multiple sequence alignment
397:Techniques and applications
145:analysis is expressed in a
10:
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436:High-throughput sequencing
264:and made use of proteins,
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2041:
2028:Wellcome Sanger Institute
1982:J. Craig Venter Institute
1928:
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1630:Phylogenetic nomenclature
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1160:10.2478/s11658-010-0010-8
1074:10.1093/zoolinnean/zlz088
826:Ahlquist, Jon E. (1999).
724:, and Doyle, J.J. (1992)
629:Phylogenetic nomenclature
442:of an organism, allowing
2011:Philippine Genome Center
571:horizontal gene transfer
2255:Molecular phylogenetics
1751:China National GeneBank
1510:Molecular phylogenetics
1460:Distance-matrix methods
1308:Molecular phylogenetics
1252:Encyclopædia Britannica
1247:Molecular phylogenetics
1186:Blaxter, M. L. (2004).
1015:10.1038/protex.2013.065
968:10.1073/pnas.74.12.5463
769:& Moritz, C. 1996.
609:Microbial phylogenetics
508:Models of DNA evolution
473:to determine a child's
241:protein electrophoresis
31:Molecular phylogenetics
1959:DNA Data Bank of Japan
1747:DNA Data Bank of Japan
1530:Phylogenetics software
1444:Probabilistic methods
1393:Long branch attraction
1204:10.1098/rstb.2003.1447
583:long-branch attraction
538:
483:genetic fingerprinting
314:
256:Theoretical background
2240:Computational biology
1755:Secondary databases:
1323:Evolutionary taxonomy
865:Page, Roderic D. M.;
771:Molecular systematics
698:Inferring phylogenies
536:
409:), ribonucleic acid (
359:DNA-DNA hybridization
348:percentage divergence
311:
250:DNA-DNA hybridization
177:Further information:
151:molecular systematics
18:Molecular systematics
1737:Sequence databases:
1482:Three-taxon analysis
1388:Phylogenetic network
635:Notes and references
451:homologous sequences
372:, and the resulting
2328:Molecular evolution
2033:Whitehead Institute
1821:Rat Genome Database
1525:Phylogenetic signal
959:1977PNAS...74.5463S
619:Molecular evolution
419:molecular structure
385:techniques such as
213:Herbert C. Dessauer
166:molecular evolution
136:) is the branch of
2270:Sequence alignment
1977:Flatiron Institute
1453:Bayesian inference
1448:Maximum likelihood
683:. Merriam-Webster.
539:
528:Bayesian inference
455:sequence alignment
357:of individuals by
315:
233:Robert K. Selander
193:Emanuel Margoliash
2310:
2309:
2265:Sequence database
1779:Protein Data Bank
1773:Other databases:
1690:
1689:
1435:Maximum parsimony
1428:Inference methods
1376:Phylogenetic tree
1198:(1444): 669–679.
1045:978-1-118-58178-0
1000:Bast, F. (2013).
875:Blackwell Science
867:Holmes, Edward C.
520:Maximum parsimony
463:mitochondrial DNA
432:Sanger sequencing
366:triangular matrix
289:an organism (its
205:Charles G. Sibley
189:Emile Zuckerkandl
147:phylogenetic tree
16:(Redirected from
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2245:List of biobanks
2209:Stockholm format
2017:Scripps Research
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1419:Ghost population
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516:Neighbor joining
504:Hamming distance
453:for genes using
370:cluster analysis
342:of a section of
319:genetic material
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1936:Broad Institute
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1099:(3): e1000602.
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614:Molecular clock
600:
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471:genetic testing
467:chloroplast DNA
424:molecular clock
399:
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229:Allan C. Wilson
227:), followed by
201:Walter M. Fitch
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767:Hillis, D. M.
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459:DNA barcoding
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440:transcriptome
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401:Every living
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262:chemotaxonomy
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237:John C. Avise
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2287:
2254:
2194:Nexus format
2189:NeXML format
2184:FASTQ format
2179:FASTA format
2167:File formats
1929:Institutions
1679:
1667:
1640:Sister group
1623:Nomenclature
1586:Autapomorphy
1581:Synapomorphy
1561:Plesiomorphy
1549:Group traits
1509:
1497:
1369:Cladogenesis
1364:Phylogenesis
1307:
1251:
1195:
1191:
1150:
1146:
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1093:PLOS Biology
1092:
1082:
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1061:
1054:
1035:
1006:Protoc. Exch
1005:
995:
950:
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911:
908:J. Mol. Biol
907:
901:
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718:Soltis, P.S.
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642:
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564:monophyletic
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344:nucleic acid
339:
335:
316:
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259:
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159:biogeography
150:
143:phylogenetic
30:
29:
2174:CRAM format
2095:(CSIR-IGIB)
1635:Crown group
1597:Group types
1328:Systematics
554:Limitations
391:jackknifing
383:Statistical
282:nucleotides
217:herpetology
185:systematics
2317:Categories
2260:Sequencing
2224:GTF format
2219:GFF format
2214:VCF format
2204:SAM format
1967:(EMBL-EBI)
1893:SOAP suite
1813:VectorBase
1775:BioNumbers
1761:Swiss-Prot
1313:Cladistics
873:. Oxford:
587:saturation
374:dendrogram
313:expressed.
299:base pairs
295:chromosome
2087:(ISCB-SC)
2057:(EMBL-AR)
1990:(MPI-CBG)
1731:Databases
1650:Supertree
1614:Polyphyly
1609:Paraphyly
1604:Monophyly
1576:Apomorphy
1556:Primitive
1499:PhyloCode
1381:Cladogram
624:PhyloCode
560:cladistic
479:forensics
475:paternity
428:evolution
355:genotypes
340:insertion
325:or other
303:haplotype
138:phylogeny
2289:Category
2159:(RECOMB)
2109:Meetings
2063:(EMBnet)
1913:Server:
1888:SAMtools
1883:PANGOLIN
1846:Software
1825:PHI-base
1817:WormBase
1787:InterPro
1669:Category
1572:Derived
1318:Taxonomy
1222:15253352
1179:20213503
1125:21423652
893:47011609
869:(1998).
813:19026976
598:See also
415:proteins
403:organism
332:outgroup
225:primates
155:taxonomy
2301:Commons
2136:(InCoB)
2081:(ISCB)
2069:(INSDC)
2051:(ASBCB)
1955:(DBCLS)
1949:(COSBI)
1863:Clustal
1809:FlyBase
1783:Ensembl
1757:UniProt
1739:GenBank
1681:Commons
1407:Lineage
1213:1693355
1170:6275913
1116:3057953
955:Bibcode
928:1100841
852:4089352
832:The Auk
413:), and
323:species
266:enzymes
219:), and
173:History
2142:(CIBB)
2130:(ISMB)
2124:(ECCB)
2101:(JSBi)
2007:(NBIC)
1996:(NCBI)
1984:(JCVI)
1973:(EMBL)
1961:(DDBJ)
1915:ExPASy
1898:TopHat
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1868:EMBOSS
1858:Bowtie
1833:GISAID
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1470:UPGMA
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1398:Clade
1250:from
848:JSTOR
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