240:
121:
467:
underscores rather than spaces in the names and uses spaces between the names and the aligned character data; it is often good practice to avoid white space within taxon names and to separate the character data from the name when generating files. Like strict phylip format files, relaxed phylip format files can be in interleaved format and include spaces and endlines within the sequence data.
730:
Maximum likelihood continuous characters and gene frequencies; estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations; also does maximum likelihood analysis of continuous characters that evolve
486:
7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083
462:
5 42 Turkey AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT Salmo_schiefermuelleri AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT H_sapiens ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Chimp AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT Gorilla
389:
The component programs of phylip use several different formats, all of which are relatively simple. Programs for the analysis of DNA sequence alignments, protein sequence alignments, or discrete characters (e.g., morphological data) can accept those data in sequential or interleaved format, as shown
398:
5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo schiAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. sapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA
407:
5 42 Turkey AAGCTNGGGC ATTTCAGGGT Salmo schiAAGCCTTGGC AGTGCAGGGT H. sapiensACCGGTTGGC CGTTCAGGGT Chimp AAACCCTTGC CGTTACGCTT Gorilla AAACCCTTGC CGGTACGCTT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA AAACCGAGGC CGGGACACTC AT AAACCATTGC CGGTACGCTT AA
361:
Each program is controlled through a menu, which asks users which options they want to set, and allows them to start the computation. The data is read into the program from a text file, which the user can prepare using any word processor or text editor (but this text file cannot be in the special
466:
The primary difference in relaxed phylip format is the absence of the 10 character limit and the removal of the need to blank fill names to reach that length (although filling names to start the character matrix at the same position can improve readability for user). This example of relaxed uses
818:
Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states (0, 1); the largest clique (or all cliques within a given size range of the largest one) are found by a fast branch and bound search method
835:
Rooted tree drawing program which plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC or
Macintosh graphics screens, and Tektronix or Digital graphics terminals.
872:
Interactive tree rearrangement program which reads in a tree (with branch lengths if needed) and allows rerooting the tree, to flip branches, to change species names and branch lengths, and then write the result out; can be used to convert between rooted and unrooted trees
809:
Interactive construction of phylogenies from discrete character data with two states (0, 1) using the Dollo or polymorphism parsimony criteria; evaluates parsimony and compatibility criteria for those phylogenies; displays reconstructed states throughout the tree
415:
Names are limited to 10 characters by default and must be blank-filled to be of that length and followed immediately by the character data using one-letter codes, although the 10 character limit name can be changed by a minor modification of the code (by changing
411:
The numbers are the number of taxa (different species in the example shown above) followed by the number of characters (aligned nucleotides or amino acids in the case of molecular sequences). Restriction site data must include the number of enzymes as well.
771:
Branch and bound mixed method which finds all of the most parsimonious phylogenies for discrete-character data with two states, for the Wagner, Camin-Sokal, and mixed parsimony criteria using the branch-and-bound method of exact search
490:
The number indicates the number of taxa and same limitations for taxon names exist. Note that this matrix is symmetric and the diagonal has values of 0 (since the distance between a taxon and itself is zero by definition).
780:
Interactive construction of phylogenies from discrete character data with two states (0, 1); evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree
801:
Finds all or most parsimonious phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of exact search
739:
Reads a tree from a tree file, and a data set with continuous characters data, and emits the independent contrasts for those characters, for use in any multivariate statistics package
567:
Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by DNA parsimony method, with compatibility and display of reconstructed ancestral bases
852:
Consensus tree program which computes trees by the majority-rule tree method, which also allows easily finding the strict consensus tree; unable to compute Adams consensus tree
327:
from FreeBSD.org. Full documentation is written for all the programs in the package and is included therein. The programs in the phylip package were written by
Professor
1127:
Minh, Bui Quang; Schmidt, Heiko A; Chernomor, Olga; Schrempf, Dominik; Woodhams, Michael D; von
Haeseler, Arndt; Lanfear, Robert (2020-05-01). Teeling, Emma (ed.).
647:
DNA distance method which computes four different distances between species from nucleic acid sequences; distances can then be used in the distance matrix programs
763:
Estimates phylogenies by some parsimony methods for discrete character data with two states (0, 1); allows using methods: Wagner, Camin-Sokal, or arbitrary mixes
627:
Estimation of phylogenies by maximum likelihood using restriction sites data; not from restriction fragments but from the presence or absence of individual sites
731:
by a
Brownian Motion model, assuming that the characters evolve at equal rates and in an uncorrelated fashion; does not account for character correlations
827:
Character recoding program which takes discrete multistate data with character state trees and emits the corresponding data set with two states (0, 1)
559:
DNA parsimony branch and bound method, finds all of the most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search
478:
method, also use a simple distance matrix format the includes only the number of taxa, their names, and numerical values for the distances:
659:, Kimura's 1983 approximation to it, or a model based on genetic code plus a constraint on changing to a different category of amino acid
655:
Protein sequence distance method which computes a distance measure for sequences, using maximum likelihood estimates based on the
Dayhoff
986:
540:
498:, an informal standard agreed to in 1986 by authors of seven major phylogeny packages. Output is written onto files with names like
339:
790:
1184:
1237:
976:
1070:
Kozlov, Alexey M; Darriba, Diego; Flouri, Tomáš; Morel, Benoit; Stamatakis, Alexandros (2019-11-01). Wren, Jonathan (ed.).
703:
Fitch-Margoliash distance matrix method with molecular clock; estimates phylogenies from distance matrix data under the
487:
Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
94:
377:
W alignment program can write data files in the PHYLIP format. Most of the programs look for the data in a file called
257:
68:
861:
747:
Genetic distance program which computes one of three different genetic distance formulas from gene frequency data
381:. If the phylip programs do not find this file, they then ask the user to type in the file name of the data file.
332:
273:
134:
39:
420:
in phylip.h and recompiling). All printable ASCII/ISO characters are allowed names, except for parentheses ("
656:
636:
454:
programs, use the phylip format or a minor modification of that format called the relaxed phylip format.
596:
1071:
905:
281:
277:
208:
203:
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DNA maximum likelihood method with molecular clock; using both dnaml and dnamlk together permits a
351:
239:
185:
695:
according to which the distances are expected to equal the sums of branch lengths between species
103:
1072:"RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference"
972:
929:
893:
584:
347:
328:
161:
27:
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952:
611:
Estimates phylogenies from protein amino acid sequences by using the maximum likelihood method
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716:
536:
475:
355:
292:
197:
141:
1129:"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era"
707:
model which is the same as the additive tree model except an evolutionary clock is assumed
1015:"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies"
688:
600:
343:
1128:
120:
909:
575:
Estimates phylogenies from nucleic acid sequence data using the compatibility criterion
1214:
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864:
symmetric difference distance between trees, which allows differences in tree topology
222:
793:
or polymorphism parsimony criteria for discrete character data with two states (0, 1)
350:, including bootstrapping and consensus trees. Data types that can be handled include
1231:
1188:
495:
447:
261:
190:
1224:: A large list of phylogeny packages with details on each one. Current count at 366.
1087:
1030:
933:
992:
896:(1981). "Evolutionary trees from DNA sequences: A maximum likelihood approach".
338:
Methods (implemented by each program) that are available in the package include
269:
667:
Distances calculated from restriction sites data or restriction fragments data
635:
For nucleic acid sequence data on four species, computes Lake's and
Cavender's
288:
34:
22:
1152:
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1095:
1038:
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1113:
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925:
844:
Unrooted tree drawing program similar to DRAWGRAM, but plots phylogenies
676:
304:
300:
284:
211:
917:
374:
324:
320:
265:
331:, of the Department of Genome Sciences and the Department of Biology,
446:
Many programs for phylogenetic analyses, including the commonly-used
316:
170:
720:
691:
method; estimates phylogenies from distance matrix data under the
551:
Estimates phylogenies of DNA sequences using the parsimony method
365:
312:
154:
619:
Protein sequence maximum likelihood method with molecular clock
308:
150:
679:, and emits multiple data sets from it by bootstrap resampling
166:
358:
and fragments, distance matrices, and discrete characters.
755:
Unordered multistate discrete-characters parsimony method
583:
Estimates phylogenies from nucleotide sequences using the
451:
443:"). The spaces embedded in the alignment are ignored.
260:
package of programs for inferring evolutionary trees (
494:
Programs that use trees as input accept the trees in
373:
format). Some sequence analysis programs such as the
362:
format of the word processor, it must instead be in
287:. Releases occur as source code, and as precompiled
217:
196:
184:
176:
160:
140:
130:
93:
67:
45:
33:
21:
675:Bootstrapping-jackknifing program; reads in a
470:The programs that use distance data, like the
8:
16:
463:AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA
1185:"PHYLIP package documentation mirror site"
238:
119:
15:
1160:
1103:
1046:
639:, which test alternative tree topologies
276:. As of version 3.696, it is licensed as
517:
947:
945:
943:
885:
272:is written in the programming language
1013:Stamatakis, Alexandros (2014-05-01).
7:
458:Relaxed phylip format (sequential):
299:(95, 98, ME, NT, 2000, XP, Vista),
14:
953:"PHYLIP general information page"
280:; versions 3.695 and older were
1133:Molecular Biology and Evolution
74:3.697 / 2 November 2014
898:Journal of Molecular Evolution
715:Implementation of the methods
1:
1088:10.1093/bioinformatics/btz305
1031:10.1093/bioinformatics/btu033
789:Estimates phylogenies by the
474:program that implements the
258:computational phylogenetics
250:PHYLogeny Inference Package
51:; 44 years ago
17:PHYLogeny Inference Package
1254:
519:Programs listed in PHYLIP
510:are in the Newick format.
535:Estimates phylogenies of
89:
63:
333:University of Washington
40:University of Washington
1222:Phylogeny Programs List
637:phylogenetic invariants
482:Phylip distance matrix:
1238:Phylogenetics software
1145:10.1093/molbev/msaa015
981:. Sinauer Associates.
428:"), square brackets ("
978:Inferring Phylogenies
597:likelihood-ratio test
506:. Trees written onto
264:). It consists of 65
76:; 9 years ago
354:, gene frequencies,
282:proprietary software
278:open-source software
268:programs, i.e., the
910:1981JMolE..17..368F
693:additive tree model
520:
403:Interleaved format:
352:molecular sequences
18:
973:Joseph Felsenstein
918:10.1007/BF01734359
585:maximum likelihood
518:
514:Component programs
394:Sequential format:
348:likelihood methods
329:Joseph Felsenstein
28:Joseph Felsenstein
23:Original author(s)
1082:(21): 4453–4455.
877:
876:
687:Fitch-Margoliash
537:peptide sequences
356:restriction sites
293:operating systems
247:
246:
49:October 1980
1245:
1218:
1217:
1215:Official website
1200:
1199:
1197:
1196:
1187:. Archived from
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1175:
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1139:(5): 1530–1534.
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1025:(9): 1312–1313.
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991:. Archived from
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717:neighbor joining
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476:neighbor-joining
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435:"), semicolon ("
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975:(August 2003).
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894:Felsenstein, J.
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862:Robinson–Foulds
689:distance matrix
601:molecular clock
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439:") and comma ("
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344:distance matrix
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46:Initial release
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11:
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1207:External links
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1076:Bioinformatics
1062:
1019:Bioinformatics
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904:(6): 368–376.
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995:on 2011-10-22
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1193:. Retrieved
1189:the original
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997:. Retrieved
993:the original
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956:. Retrieved
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527:Description
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431:"), colon ("
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401:
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370:
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337:
256:) is a free
253:
249:
248:
177:Available in
35:Developer(s)
705:ultrametric
603:hypothesis
385:File format
335:, Seattle.
289:executables
270:source code
262:phylogenies
227:.washington
209:proprietary
204:open-source
114:/sourcecode
108:.washington
1195:2006-03-24
999:2006-03-24
958:2010-02-14
880:References
657:PAM matrix
539:using the
295:including
131:Written in
95:Repository
81:2014-11-02
1153:0737-4038
1096:1367-4803
1039:1460-2059
857:treedist
849:consense
841:drawtree
832:drawgram
798:dolpenny
736:contrast
712:neighbor
664:restdist
652:protdist
632:dnainvar
556:dnapenny
541:parsimony
532:protpars
371:text only
340:parsimony
291:for many
225:.genetics
223:evolution
106:.genetics
104:evolution
1232:Category
1171:32011700
1114:31070718
1057:24451623
806:dolmove
744:gendist
677:data set
672:seqboot
644:dnadist
599:for the
572:dnacomp
564:dnamove
548:dnapars
472:neighbor
305:Mac OS 9
301:Mac OS 8
285:freeware
266:portable
212:freeware
162:Platform
1162:7182206
1105:6821337
1048:3998144
934:8024924
926:7288891
906:Bibcode
869:retree
824:factor
815:clique
786:dollop
727:contml
700:kitsch
624:restml
616:promlk
592:dnamlk
587:method
543:method
508:outtree
504:outtree
500:outfile
452:IQ-TREE
424:" and "
418:nmlngth
390:below.
375:Clustal
325:FreeBSD
323:); and
321:Red Hat
297:Windows
231:/phylip
218:Website
198:License
180:English
147:Windows
112:/phylip
79: (
56:1980-10
54: (
1169:
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1094:
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