PHYLIP (PHYlogeny Inference Programs)

biol4230 Friday, March 2, 2018

Bill Pearson wrp@virginia.edu 4-2818 Pinn 6-057

PHYLIP via EMBOSS

• Tree building:
– distance: (f)fitch,(f)kitsch, needs (f)dnadist or
(f)protdist first
– parsimony: (f)dnapars, (f)protpars
– Likelihood: (f)dnaml, (f)dnamlk, (f)protml
• Tree drawing:
– (f)drawtree – unrooted
– (f)drawgram – draws a tree
• Utilities:
– (f)consense – show consensus tree
– retree – reroot trees (use interactively)

fasta.bioch.virginia.edu/biol4230 1

PHYLIP (PHYlogeny Inference Programs)

• A package of programs developed by Joe

Felsenstein; available since 1980
• Written in 'C' for a command line interface
• Available for most popular computers
• Provides a diverse variety of methods for
sequence and other data

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Phylip 3.69

Advantages Disadvantages
• Free (GNU license) • Much slower than PAUP
• Runs on all major • Search strategy less
platforms comprehensive
• Good documentation • Primitive command-line
• Well known/widely used interface (user hostile)
• Possible to automate • Much file renaming
required
• File formats supported by
other packages • Cannot read NEXUS files

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PHYLIP Tree-building programs

• Parsimony:
– dnaparse - parsimony (protparse)
– No branch lengths on trees
• Distance Methods
– dnadist, protdist – produce corrected
distance matrices
– fitch, kitsch – Fitch-Margoliash distance
(clock, kitsch) trees from distances
– Neighbor – Neighbor-joining trees (no explicit
optimization criterion)

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 PHYLIP Tree-building programs
• Maximum Likelihood
– dnaml, dnamlk - DNA maximum likelihood
– proml, promlk - protein maximum likelihood
– *mlk methods assume evolutionary clock (all
branches end at same level (time)

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PHYLIP Program Data/Output

infile
intree outfile
Phylip outtree
weights
Program plotfile
categories
fontfile

• The phylip programs re-use the same file names: "infile", "outfile", every
time a program is used. In current versions, if the input file is not present, it
is prompted for, and if the output file is present, one is warned before over-
writing it.
• However, it is easy to analyse the wrong data (old "infile") and over write
(or mis-name) the output file.
• Develop a protocol for ensuring that file names make sense. NEVER use
infile and outfile, outree. This can be difficult. Scripts help.
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 PHYLIP via EMBOSS

• EMBOSS (European Molecular Biology lab

Open Software Suite)
– command line options
– interactive when needed (sometimes annoying)
– use –help
• EMBOSS PHYLIP:
– f+PHYLIP name: fdnadist, fconsense, ffitch,
fkitsch, etc

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PHYLIP sequence format (interleaved)

Number Length of
of taxa alignment

7 112
Bovine CCAAACCTGT CCCCACCATC TAACACCAAC CCACATATAC AAGCTAAACC AAAAATACCA
Mouse CCAAAAAAAC ATCCAAACAC CAACCCCAGC CCTTACGCAA TAGCCATACA AAGAATATTA
Gibbon CTATACCCAC CCAACTCGAC CTACACCAAT CCCCACATAG CACACAGACC AACAACCTCC
Orang CCCCACCCGT CTACACCAGC CAACACCAAC CCCCACCTAC TATACCAACC AATAACCTCT
Gorilla CCCCATTTAT CCATAAAAAC CAACACCAAC CCCCATCTAA CACACAAACT AATGACCCCC
Chimp CCCCATCCAC CCATACAAAC CAACATTACC CTCCATCCAA TATACAAACT AACAACCTCC
Human CCCCACTCAC CCATACAAAC CAACACCACT CTCCACCTAA TATACAAATT AATAACCTCC

CCCCAGCCCA ACACCCTTCC ACAAATCCTT AATATACGCA CCATAAATAA CA

TCCCACCAAA TCACCCTCCA TCAAATCCAC AAATTACACA ACCATTAACC CA
GCACGCCAAG CTCTCTACCA TCAAACGCAC AACTTACACA TACAGAACCA CA
ACACCCTAAG CCACCTTCCT CAAAATCCAA AACCCACACA ACCGAAACAA CA
ACACCTCAAT CCACCTCCCC CCAAATACAC AATTCACACA AACAATACCA CA
ACATCTTGAC TCGCCTCTCT CCAAACACAC AATTCACGCA AACAACGCCA CA
ACACCTTAAC TCACCTTCTC CCAAACGCAC AATTCGCACA CACAACGCCA CA

use EMBOS seqret to convert to PHYLIP format (-osformat2 phylip)

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 PHYLIP Tree representation (NEWICK)

Taxa Branch
label Length

(Mouse:0.87231,Bovine:0.49807,(Gibbon:0.25930,(Orang:0.24
166, (Gorilla:0.12322,(Chimp:0.13846,
Human:0.08571):0.06026):0.04405):0.10815):0.39538);
(Mouse:0.87558,Bovine:0.49718,(Gibbon:0.25698,(Orang:0.24
477, ((Gorilla:0.16328,Chimp:0.13802):0.01842,
Human:0.08495):0.06610):0.10637):0.39287);
(Mouse:0.87819,Bovine:0.49461,(Gibbon:0.25837,(Orang:0.24
161, (Chimp:0.13941,(Gorilla:0.16639,
Human:0.09533):0.00616):0.06709):10938):0.39630);

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PHYLIP Tree representation (NEWICK)

Gibbon Orang

Gorilla

Chimp
Human
Bovine

Mouse
(Mouse:0.87231,Bovine:0.49807,(Gibbon:0.25930,(Orang:0.24
166, (Gorilla:0.12322,(Chimp:0.13846,
Human:0.08571):0.06026):0.04405):0.10815):0.39538);
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 Tree-analysis/display
• Tree comparison:
– (f)consense – Calculate consensus tree from
bootstraps
– (f)treedist – compare trees by "partition
distance"
• Manipulation
– retree – flip nodes, re-root, re-arrange – run
interactively
• Display
– (f)drawgram – draw "tree-like" tree
– (f)drawtree – draw unrooted tree

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Running PHYLIP
15 675
GTM1_HUMAN ---------- --ATGCCCAT GATACTGGGG TACTGGGACA TCCGCGGGCT
infile GTM2_HUMAN ---------- --ATGCCCAT GACACTGGGG TACTGGAACA TCCGCGGGCT
GTM3_HUMAN ATGTCGTGCG AGTCGTCTAT GGTTCTCGGG TACTGGGATA TTCGTGGGCT
gstm_n.phy GTM4_HUMAN ---------- --ATGTCCAT GACACTGGGG TACTGGGACA TCCGCGGGCT
GTM5_HUMAN ---------- --ATGCCCAT GACTCTGGGG TACTGGGACA TCCGTGGGCT
GTM1_MOUSE ---------- --ATGCCTAT GATACTGGGA TACTGGAACG TCCGCGGACT
GTM2_MOUSE ---------- --ATGCCTAT GACACTAGGT TACTGGGACA TCCGTGGGCT
GTM3_MOUSE ---------- --ATGCCTAT GACACTGGGC TATTGGAACA CCCGCGGACT
GTM5_MOUSE ATGTCATCCA AGTCT---AT GGTTCTGGGT TACTGGGATA TCCGCGGGCT
GTM1_RAT ---------- --ATGCCTAT GATACTGGGA TACTGGAACG TCCGCGGGCT
GTM2_RAT ---------- --ATGCCTAT GACACTGGGT TACTGGGACA TCCGTGGGCT
GTM3_RAT ---------- --ATGCCCAT GACACTGGGT TACTGGGACA TCCGTGGGCT
GTMU_CRILO ---------- --ATGCCTAT GATACTGGGA TACTGGAATG TCCGCGGTCT
GTMU_MESAU ---------- --ATGCCTGT GACACTGGGT TACTGGGACA TCCGTGGGCT
GTM2_CHICK ---------- --ATGGTGGT CACGTTGGGT TATTGGGACA TCCGCGGGTT

GGCCCACGCC ATCCGCCTGC TCCTGGAATA CACAGACTCA AGCTATGAGG

GGCCCATTCC ATCCGCCTGC TCCTGGAATA CACAGACTCA AGCTACGAGG
GGCGCACGCC ATCCGCCTGC TCCTGGAGTT CACGGATACC TCTTATGAGG
GGCCCACGCC ATCCGCCTGC TCCTGGAATA CACAGACTCA AGCTACGAGG
GGCCCACGCC ATCCGCTTGC TCCTGGAATA CACAGACTCA AGCTATGTGG
GACACACCCG ATCCGCATGC TCCTGGAATA CACAGACTCA AGCTATGATG
GGCTCACGCC ATCCGCCTGC TCCTGGAATA CACAGACACA AGCTATGAGG
GACTCACTCC ATCCGCTTGC TCCTGGAATA CACAGATTCA AGCTATGAGG
GGCTCATGCT ATCCGCATGC TTCTGGAGTT TACTGATACC AGCTATGAGG
GACACACCCG ATCCGCCTGC TCCTGGAATA CACAGACTCA AGCTATGAGG
GGCTCACGCC ATTCGCCTGT TCCTGGAGTA TACAGACACA AGCTATGAGG
AGCGCATGCC ATCCGCCTGC TCCTGGAATA CACAGACTCG AGCTATGAGG
GACAAACCCC ATCCGCCTGC TCCTGGAATA CACAGACTCA AGCTATGAGG
GGCTCATGCC ATCCGCCTGC TCTTGGAGTA CACAGACACA AGCTATGAGG
GGCCCACGCC ATCCGCCTGC TGCTGGAGTA CACCGAGACC CCCTACCAGG

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 Running PHYLIP - dnaml
$ fdnaml -help
Standard (Mandatory) qualifiers:
[-sequence] seqsetall File containing one or more sequence
alignments
[-intreefile] tree Phylip tree file (optional)
[-outfile] outfile [*.fdnaml] Phylip dnaml program output file

Additional (Optional) qualifiers (* if not always prompted):

-ncategories integer [1] Number of substitution rate categories
(Integer from 1 to 9)
-weights properties Weights file
* -njumble integer [0] Number of times to randomise (Integer 0
or more)
* -seed integer [1] Random number seed between 1 and 32767
(must be odd) (Integer from 1 to 32767)
* -global boolean [N] Global rearrangements
-outgrno integer [0] Species number to use as outgroup (Integer
• -outtreefile outfile [*.fdnaml] Phylip tree output file (optional)

General qualifiers:
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose

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Running PHYLIP – (f)dnaml

Nucleic acid sequence Maximum Likelihood method, version 3.63
Settings for this run:
U Search for best tree? Yes
T Transition/transversion ratio: 2.0000
F Use empirical base frequencies? Yes
C One category of sites? Yes
R Rate variation among sites? constant rate
W Sites weighted? No
S Speedier but rougher analysis? Yes
G Global rearrangements? No
J Randomize input order of sequences? No. Use input order
O Outgroup root? Yes, at sequence number 15
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? ANSI
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Write out trees onto tree file? Yes
5 Reconstruct hypothetical sequences? No
Y to accept these or type the letter for one to change
j
Random number seed (must be odd)?
123
Number of times to jumble?
5
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 Running PHYLIP – (f)dnaml
Nucleic acid sequence Maximum Likelihood method, version 3.63
Empirical Base Frequencies:
A 0.25824 Ln Likelihood = -4967.04025
C 0.25662
G 0.25997
T(U) 0.22516 Betwn And Length Approx. Confid. Limits
Transition/transversion ratio = 2.000000 ----- --- ------ ------- ------- ------

+---GTM3_MOUSE 11 GTM2_CHICK 0.31594 ( 0.25746, 0.37441) **

+--8 11 3 0.08672 ( 0.05406, 0.11939) **
| | +--GTMU_CRILO 3 4 0.02793 ( 0.01168, 0.04422) **
| +--9 4 2 0.02634 ( 0.01094, 0.04173) **
| | +-GTM1_MOUSE 2 8 0.03562 ( 0.01808, 0.05315) **
+--2 +-12 8 GTM3_MOUSE 0.08136 ( 0.05732, 0.10551) **
| | +-GTM1_RAT 8 9 0.01699 ( 0.00496, 0.02902) **
| | 9 GTMU_CRILO 0.05525 ( 0.03583, 0.07467) **
| | +---GTMU_MESAU 9 12 0.01836 ( 0.00619, 0.03053) **
+--4 +--5 12 GTM1_MOUSE 0.03072 ( 0.01641, 0.04505) **
| | | +--GTM2_RAT 12 GTM1_RAT 0.03335 ( 0.01837, 0.04833) **
| | +--1 2 5 0.04458 ( 0.02524, 0.06391) **
| | +GTM2_MOUSE 5 GTMU_MESAU 0.07139 ( 0.04896, 0.09383) **
| | 5 1 0.02084 ( 0.00814, 0.03354) **
+----3 +----GTM3_RAT 1 GTM2_RAT 0.04346 ( 0.02629, 0.06055) **
| | 1 GTM2_MOUSE 0.01543 ( 0.00448, 0.02638) **
| | +---GTM2_HUMAN 4 GTM3_RAT 0.08214 ( 0.05771, 0.10667) **
| | | 3 6 0.02335 ( 0.00714, 0.03966) **
| +--6 +--GTM4_HUMAN 6 GTM2_HUMAN 0.07147 ( 0.04929, 0.09368) **
| | +-10 6 7 0.00694 ( zero, 0.01543) *
| +--7 +-GTM1_HUMAN 7 10 0.01316 ( 0.00296, 0.02336) **
| | 10 GTM4_HUMAN 0.05475 ( 0.03560, 0.07398) **
| +---GTM5_HUMAN 10 GTM1_HUMAN 0.03047 ( 0.01614, 0.04490) **
| 7 GTM5_HUMAN 0.06349 ( 0.04281, 0.08419) **
| +----GTM5_MOUSE 11 13 0.13085 ( 0.09317, 0.16853) **
11------13 13 GTM5_MOUSE 0.07982 ( 0.05403, 0.10560) **
| +---GTM3_HUMAN 13 GTM3_HUMAN 0.06202 ( 0.03845, 0.08568) **
|
+------------------GTM2_CHICK * = significantly positive, P < 0.05
** = significantly positive, P < 0.01
fasta.bioch.virginia.edu/biol4230
remember: (although rooted by outgroup) this is an unrooted tree! 15

Running PHYLIP – (f)dnapars

DNA parsimony algorithm, version 3.63

Setting for this run:

U Search for best tree? Yes
S Search option? More thorough search
V Number of trees to save? 10000
J Randomize input order of sequences? No. Use input order
O Outgroup root? Yes, at sequence number 15
T Use Threshold parsimony? No, use ordinary parsimony
N Use Transversion parsimony? No, count all steps
W Sites weighted? No
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? ANSI
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Print out steps in each site No
5 Print sequences at all nodes of tree No
6 Write out trees onto tree file? Yes

Y to accept these or type the letter for one to change

Y

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 Running PHYLIP – (f)dnapars
DNA parsimony algorithm, version 3.63 requires a total of 913.000

3 trees in all found between and length

------- --- ------
+-----------GTM2_CHICK 2 GTM2_CHICK 0.203366
| 2 8 0.131035
| +---GTM5_MOUSE 8 GTM5_MOUSE 0.075672
2-------8 8 GTM3_HUMAN 0.061172
| +---GTM3_HUMAN 2 5 0.085438
| 5 11 0.026262
| +---GTM3_RAT 11 GTM3_RAT 0.067351
| | 11 6 0.027000
| | +--GTMU_MESAU 6 13 0.038716
| +-11 +-13 13 GTMU_MESAU 0.062522
| | | | | +-GTM2_RAT 13 10 0.020370
| | | | +-10 10 GTM2_RAT 0.037725
| | +--6 +GTM2_MOUSE 10 GTM2_MOUSE 0.017584
| | | 6 7 0.032519
| | | +---GTM3_MOUSE 7 GTM3_MOUSE 0.067937
| | +--7 7 12 0.020952
| | | +-GTMU_CRILO 12 GTMU_CRILO 0.049136
+----5 +-12 12 9 0.018272
| | +GTM1_RAT 9 GTM1_RAT 0.031111
| +--9 9 GTM1_MOUSE 0.028148
| +GTM1_MOUSE 5 1 0.030898
| 1 4 0.009778
| +--GTM5_HUMAN 4 GTM5_HUMAN 0.056824
| +--4 4 GTM2_HUMAN 0.061695
| | +--GTM2_HUMAN 1 3 0.013210
+--1 3 GTM4_HUMAN 0.047152
| +--GTM4_HUMAN 3 GTM1_HUMAN 0.030750
+--3
+-GTM1_HUMAN

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(f)dnapars – three alternate trees

(GTM2_CHICK:0.20337,(GTM5_MOUSE:0.07567,GTM3_HUMAN:0.06117):0.13103,
((GTM3_RAT:0.06735,((GTMU_MESAU:0.06252,(GTM2_RAT:0.03772,GTM2_MOUSE:0.01758):0.02037):0.
03872,
(GTM3_MOUSE:0.06794,(GTMU_CRILO:0.04914,(GTM1_RAT:0.03111,GTM1_MOUSE:0.02815):0.01827):0.
02095):0.03252):0.02700):0.02626,
((GTM5_HUMAN:0.05682,GTM2_HUMAN:0.06169):0.00978,(GTM4_HUMAN:0.04715,
GTM1_HUMAN:0.03075):0.01321):0.03090):0.08544)[0.3333];

(GTM2_CHICK:0.19762,(GTM5_MOUSE:0.07698,GTM3_HUMAN:0.05942):0.13647,
(((GTMU_MESAU:0.06103,(GTM2_RAT:0.03807,GTM2_MOUSE:0.01723):0.02135):0.03741,
(GTM3_MOUSE:0.06916,(GTMU_CRILO:0.04806,(GTM1_RAT:0.03111,GTM1_MOUSE:0.02815):0.01935):0.
02106):0.03236):0.02522,
(GTM3_RAT:0.06150,(GTM2_HUMAN:0.05333,(GTM5_HUMAN:0.05213,(GTM4_HUMAN:0.04975,
GTM1_HUMAN:0.02815):0.01713):0.01605):0.04058):0.02860):0.08532)[0.3333];

(GTM2_CHICK:0.20335,(GTM5_MOUSE:0.07591,GTM3_HUMAN:0.06098):0.13099,
((GTM3_RAT:0.06487,((GTMU_MESAU:0.06237,(GTM2_RAT:0.03787,GTM2_MOUSE:0.01744):0.02037):0.
03904,
(GTM3_MOUSE:0.06806,(GTMU_CRILO:0.04899,(GTM1_RAT:0.03111,GTM1_MOUSE:0.02815):0.01842):0.
02098):0.03254):0.02944):0.02617,
(GTM2_HUMAN:0.05754,(GTM5_HUMAN:0.05427,(GTM4_HUMAN:0.05030,GTM1_HUMAN:0.02760):0.01481):
0.01128):0.03306):0.08668)[0.3333];

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 Running PHYLIP – distance methods

• Distance methods do not work on alignments,

they work on distances
– take alignment and build (corrected) distance
matrix fdnadist, fprotdist
– take distance matrix, build tree using ffitch (no
–evolutionary clock), or fkitsch (clock-like tree)
– fneighbor for speed

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Running PHYLIP – (f)dnadist

Nucleic acid sequence Distance Matrix program, version 3.63

Settings for this run:

D Distance (F84, Kimura, Jukes-Cantor, LogDet)? F84
G Gamma distributed rates across sites? No
T Transition/transversion ratio? 2.0
C One category of substitution rates? Yes
W Use weights for sites? No
F Use empirical base frequencies? Yes
L Form of distance matrix? Square
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? ANSI
1 Print out the data at start of run No
2 Print indications of progress of run Yes

Y to accept these or type the letter for one to change

y
Distances calculated for species
GTM1_HUMAN ..............
GTM2_HUMAN .............
GTM3_HUMAN ............
GTM4_HUMAN ...........
GTM5_HUMAN ..........
GTM1_MOUSE .........
GTM2_MOUSE ........
GTM3_MOUSE .......
. . .
Distances written to file "gstm_n.ddist"
Done.
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 Running PHYLIP – (f)dnadist

15
GTM1_HUMAN 0.000000 0.111515 0.328043 0.084938 0.098515 0.202847
0.160670 0.222157 0.323212 0.195992 0.188005 0.176254 0.169073
0.202499 0.472135
GTM2_HUMAN 0.111515 0.000000 0.370425 0.122881 0.135281 0.234489
0.198432 0.246131 0.367307 0.220479 0.235718 0.162609 0.200569
0.245624 0.499002
GTM3_HUMAN 0.328043 0.370425 0.000000 0.330864 0.337744 0.395844
0.350801 0.407140 0.141206 0.397266 0.389013 0.385259 0.364146
0.386434 0.489052
GTM4_HUMAN 0.084938 0.122881 0.330864 0.000000 0.131796 0.233678
0.187505 0.236442 0.337068 0.235722 0.213963 0.182756 0.204816
0.204302 0.452330
GTM5_HUMAN 0.098515 0.135281 0.337744 0.131796 0.000000 0.230120
0.186003 0.230817 0.353029 0.215696 0.218532 0.174287 0.201916
0.216947 0.470660
GTM1_MOUSE 0.202847 0.234489 0.395844 0.233678 0.230120 0.000000
0.160969 0.116636 0.395293 0.062703 0.200109 0.200296 0.105091
0.202873 0.486157
GTM2_MOUSE 0.160670 0.198432 0.350801 0.187505 0.186003 0.160969
0.000000 0.172174 0.370651 0.159042 0.058864 0.178584 0.146716
0.103994 0.474313
. . .

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Running PHYLIP – (f)fitch

Fitch-Margoliash method version 3.63

Settings for this run:

D Method (F-M, Minimum Evolution)? Fitch-Margoliash
U Search for best tree? Yes
P Power? 2.00000
- Negative branch lengths allowed? No
O Outgroup root? Yes, at species number 15
L Lower-triangular data matrix? No
R Upper-triangular data matrix? No
S Subreplicates? No
G Global rearrangements? Yes
J Randomize input order of species? No. Use input order
M Analyze multiple data sets? No
0 Terminal type (IBM PC, ANSI, none)? ANSI
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Write out trees onto tree file? Yes

Y to accept these or type the letter for one to change

y

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 Running PHYLIP – (f)fitch
+---GTM5_MOUSE 15 Populations
+-------7 Fitch-Margoliash method version 3.63
! +---GTM3_HUMAN __ __ 2
! \ \ (Obs - Exp)
! +---GTM5_HUMAN Sum of squares = /_ /_ ------------
! +-2 2
! ! ! +---GTM2_HUMAN i j Obs
! ! +-3 Negative branch lengths not allowed
! ! ! +--GTM4_HUMAN global optimization
! ! +-1
13---4 +-GTM1_HUMAN
! !
! ! +----GTM3_RAT Average percent standard deviation = 4.78966
! ! !
! ! ! +---GTMU_MESAU Between And Length
! +-10 +-12 ------- --- ------
! ! ! ! +--GTM2_RAT 13 7 0.13286
! ! ! +-9 7 GTM5_MOUSE 0.07381
! +-5 +GTM2_MOUSE 7 GTM3_HUMAN 0.06739
! ! 13 4 0.05956
! ! +-GTMU_CRILO 4 2 0.02688
! +-11 2 GTM5_HUMAN 0.06200
! ! +----GTM3_MOUSE 2 3 0.00263
! +-6 3 GTM2_HUMAN 0.06785
! ! +-GTM1_RAT 3 1 0.00736
! +-8 1 GTM4_HUMAN 0.05312
! +-GTM1_MOUSE . . .
!
+-----------------GTM2_CHICK
remember: (although rooted by outgroup) this is an unrooted tree!
Sum of squares = 0.47717
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Drawing trees- (f)drawtree

wrpmbp 29% drawtree Most common problem missing fontfile:
DRAWTREE from PHYLIP version 3.67 cp $HPC_SLIB/seqprg/data/font1 fontfile
Drawtree: can't find input tree file "intree"
Please enter a new file name> gstm_n.fdd_tree
Reading tree ... 2nd most common problem:
Tree has been read. overwriting/renaming plotfile
Loading the font ...
Font loaded.

Unrooted tree plotting program version 3.67

Here are the settings:

0 Screen type (IBM PC, ANSI)? (none)

P Final plotting device: Postscript printer
V Previewing device: Macintosh graphics screen
B Use branch lengths: Yes
L Angle of labels: branch points to Middle of label
R Rotation of tree: 90.0
I Iterate to improve tree: Equal-Daylight algorithm
D Try to avoid label overlap? No
S Scale of branch length: Automatically rescaled
C Relative character height: 0.3333
F Font: Times-Roman
M Horizontal margins: 1.65 cm
M Vertical margins: 2.16 cm
# Page size submenu: one page per tree

Y to accept these or type the letter for one to change

y

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 Drawing trees- (f)drawtree
GTMU MESAU
GTM3 RAT

GTM2 RAT
GTM4 HUMAN
GTM1 HUMAN

GTM2 MOUSE
GTM2 HUMAN

GTMU CRILO

GTM5 HUMAN
GTM3 MOUSE

GTM1 RAT

GTM1 MOUSE

GTM3 HUMAN

GTM5 MOUSE

GTM2 CHICK

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Drawing trees- (f)drawgram

GTM2 CHICK

GTM3 HUMAN
GTM4 HUMAN
GTM1 HUMAN
GTM5 HUMAN
GTM2 HUMAN

GTMU MESAU
GTM5 MOUSE

GTM2 MOUSE

GTM1 MOUSE

GTM3 MOUSE
GTMU CRILO

GTM2 CHICK
GTM3 RAT
GTM2 RAT

GTM1 RAT
GTM3 MOUSE
GTM5 MOUSE
GTM3 HUMAN

GTMU MESAU

GTM1 MOUSE
GTMU CRILO
GTM2 HUMAN

GTM2 MOUSE

GTM1 RAT
GTM4 HUMAN
GTM5 HUMAN

GTM2 RAT
GTM1 HUMAN
GTM3 RAT

fitch kitcsh -
(evolutionary clock)

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 Evaluating trees- (f)consense
Consensus tree program, version 3.63

Settings for this run:

C Consensus type (MRe, strict, MR, Ml): Majority rule (extended)
O Outgroup root: Yes, at species number 15
R Trees to be treated as Rooted: No
T Terminal type (IBM PC, ANSI, none): ANSI
1 Print out the sets of species: Yes
2 Print indications of progress of run: Yes
3 Print out tree: Yes
4 Write out trees onto tree file: Yes

Are these settings correct? (type Y or the letter for one to change)
y

fasta.bioch.virginia.edu/biol4230 27

Evaluating trees- (f)consense

Consensus tree program, version 3.63
Sets included in the consensus tree
Species in order:
Set (species in order) How many times out of 3.00
1. GTM5 MOUSE
2. GTM3 HUMAN .......... ****. 3.00
3. GTM5 HUMAN ..****.... ..... 3.00
4. GTM2 HUMAN .......... ..**. 3.00
5. GTM4 HUMAN ........** ..... 3.00
6. GTM1 HUMAN .......*** ****. 3.00
7. GTM3 RAT ..******** ****. 3.00
8. GTMU MESAU ....**.... ..... 3.00
9. GTM2 RAT .......*** ..... 3.00
10. GTM2 MOUSE **........ ..... 3.00
......**** ****. 2.67
11. GTMU CRILO .......... .***. 2.00
12. GTM3 MOUSE ...***.... ..... 2.00
13. GTM1 RAT
14. GTM1 MOUSE
15. GTM2 CHICK Sets NOT included in consensus tree:

Set (species in order) How many times out of 3.00

.......... *.**. 1.00

..*.**.... ..... 0.67
..**...... ..... 0.33
..*****... ..... 0.33

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 Evaluating trees- (f)consense
Extended majority rule consensus tree +------GTM1 RAT
+--3.0-|
CONSENSUS TREE: +--2.0-| +------GTM1 MOUSE
the numbers on the branches indicate the number | |
of times the partition of the species into the two sets +--3.0-| +-------------GTM3 MOUSE
which are separated by that branch occurred | |
among the trees, out of 3.00 trees +--3.0-| +--------------------GTMU CRILO
| |
| | +-------------GTMU MESAU
| +---------3.0-|
+--2.7-| | +------GTM2 RAT
| | +--3.0-|
| | +------GTM2 MOUSE
| |
| +----------------------------------GTM3 RAT
+--3.0-|
| | +------GTM1 HUMAN
| | +--3.0-|
| | +--2.0-| +------GTM4 HUMAN
| | | |
+------| +----------------3.0-| +-------------GTM2 HUMAN
| | |
| | +--------------------GTM5 HUMAN
| |
| | +------GTM3 HUMAN
| +-------------------------------------3.0-|
| +------GTM5 MOUSE
|
+-------------------------------------------------------GTM2 CHICK

remember: (though rerooted by outgroup) this is an unrooted tree!

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Putting it all together, the User tree

• The problem:
– the (f)consense program produces the best
consensus tree, but the branches reflect the
consensus frequencies, not the evolutionary
branch lengths
• The solution:
– give consensus tree to fdnaml or ffitch using
the 'U' user tree option – calculates branches for
a single tree, does not do a search (fast)

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 User tree – (f)dnaml
Nucleic acid sequence Maximum Likelihood method, version 3.63

Settings for this run:

U Search for best tree? No, use user trees in input file
L Use lengths from user trees? No
T Transition/transversion ratio: 2.0000
F Use empirical base frequencies? Yes
C One category of sites? Yes
R Rate variation among sites? constant rate
W Sites weighted? No
O Outgroup root? No, use as outgroup species 1
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? ANSI
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Write out trees onto tree file? Yes
5 Reconstruct hypothetical sequences? No

Y to accept these or type the letter for one to change

Asks for infile (alignment) and intree (consensus tree)

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User tree – dnaml

User-defined tree:
+-GTM1_RAT
+--7
+--6 +-GTM1_MOUSE
| |
+--5 +----GTM3_MOUSE
| |
+--4 +--GTMU_CRILO
| |
| | +---GTMU_MESAU Consensus tree DNAML:
| +--8 Ln Likelihood = -4977.65455
+--3 | +--GTM2_RAT
| | +--9
| | +GTM2_MOUSE Original best DNAML:
| | Ln Likelihood = -4967.04025
| +----GTM3_RAT
+----2
| | +-GTM1_HUMAN
| | +-12
| | +-11 +--GTM4_HUMAN
| | | |
| +-10 +---GTM2_HUMAN
| |
| +---GTM5_HUMAN
|
| +---GTM3_HUMAN
1------13
| +----GTM5_MOUSE
|
+------------------GTM2_CHICK
remember: (although rooted by outgroup) this is an unrooted tree!
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Phylip for dummies
• Programs for Parsimony, Distance, and
Maximum Likelihood
• infile/outfile/outtree/intree
– either always change, or never use
– Use EMBOS (f) programs
• (f)consense to build consensus tree (but
invalid branch lengths)
• User tree to calculate branch lengths for
consensus tree
• (f)drawtree for non-trees, (f)drawgram
for trees

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