View source for Mm9 multiple alignment

==Mouse Mm9 multiple alignment/conservation track==

<TABLE BORDER=0>
<TR><TD>
To avoid artifacts in downstream processing of the UCSC multiple alignments, it is important to be careful on the use of the parameters used in the blastz processing pipeline.  There are a number of steps in the pipeline and a variety of tunable parameters involved.  This page will track the various parameters used in the alignments as they proceed toward the completion of a multiple alignment conservation track on the mm9 mouse (NCBI build 37) assembly

The chrom count in the table below does not include haplotypes, chr*_random, chrUn or chrM unless chrUn or scaffolds are the only sequences for that assembly.

The genome size has the same limitation as the chrom count, no randoms.

Tree distances are from the hg18 28-way measurements, with ponAbe1 and calJac1 manually inserted into the tree. 

I believe we use "syntenic" nets on the organisms that are assembled
into chromosomes.

1 Mb = 1000 * 1000 = 1,000,000 bases

</TD><TD>
[[Image:Mm9_30way.gif|frame|30-way phylogenetic tree]]
</TD></TR></TABLE>

==axtChain parameters and end results==

<TABLE BORDER=1>
<TR>
  <TH>name db</TH>
  <TH>chrom<BR>count (*)</TH>
  <TH>genome<BR>size</TH>
  <TH>tree<BR>distance</TH>
  <TH>axtChain<BR>minScore</TH>
  <TH>axtChain<BR>linearGap</TH>
  <TH>% of mm9<BR>matched</TH>
  <TH>% of other<BR>matched by mm9</TH>
  <TH>done</TH>
</TR>

<TR>
  <TH>mouse mm9<BR>self alignment</TH>
  <TD>21</TD>
  <TD>2654 Mb</TD>
  <TD>0.0</TD> 
  <TD>10000</TD>
  <TD>medium</TD>
  <TD>14.458</TD>
  <TD>N/A</TD>
  <TD>2007-08-31</TD>
</TR>

<TR>
  <TH>rat rn4</TH>
  <TD>21</TD>
  <TD>2718 Mb</TD>
  <TD>0.160657</TD> 
  <TD>5000</TD>
  <TD>medium</TD>
  <TD>68.357</TD>
  <TD>69.541</TD>
  <TD>re-running 31 Aug</TD>
</TR>

<TR>
  <TH>human hg18</TH>
  <TD>24</TD>
  <TD>3080 Mb</TD>
  <TD>0.452619</TD> 
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>38.499</TD>
  <TD>35.201</TD>
  <TD>2007-08-16</TD>
<TR>

<TR>
  <TH>Rhesus rheMac2</TH>
  <TD>22</TD>
  <TD>2864 Mb</TD>
  <TD>0.452745</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Orangutan ponAbe1</TH>
  <TD>79553</TD>
  <TD>3240 Mb</TD>
  <TD>0.453809</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Marmoset calJac1</TH>
  <TD>49724</TD>
  <TD>3029 Mb</TD>
  <TD>0.454272</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Chimp panTro2</TH>
  <TD>25</TD>
  <TD>3175 Mb</TD>
  <TD>0.454514</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>GuineaPig cavPor2</TH>
  <TD>295514</TD>
  <TD>3403 Mb</TD>
  <TD>0.479871</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Horse equCab1</TH>
  <TD>32</TD>
  <TD>2056 Mb</TD>
  <TD>0.479871</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>TreeShrew tupBel1</TH>
  <TD>150851</TD>
  <TD>3660 Mb</TD>
  <TD>0.494934</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Bushbaby otoGar1</TH>
  <TD>120882</TD>
  <TD>3420 Mb</TD>
  <TD>0.498957</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Armadillo dasNov1</TH>
  <TD>304391</TD>
  <TD>3856 Mb</TD>
  <TD>0.517360</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Rabbit oryCun1</TH>
  <TD>215471</TD>
  <TD>3464 Mb</TD>
  <TD>0.519779</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Cat felCat3</TH>
  <TD>217790</TD>
  <TD>4045 Mb</TD>
  <TD>0.530610</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Dog canFam2</TH>
  <TD>39</TD>
  <TD>2445 Mb</TD>
  <TD>0.533544</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>32.362</TD>
  <TD>34.891</TD>
  <TD>2007-09-05</TD>
</TR>

<TR>
  <TH>Elephant loxAfr1</TH>
  <TD>233134</TD>
  <TD>3707 Mb</TD>
  <TD>0.536627</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Cow bosTau3</TH>
  <TD>30</TD>
  <TD>2434 Mb</TD>
  <TD>0.540852</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Hedgehog eriEur1</TH>
  <TD>379801</TD>
  <TD>3367 Mb</TD>
  <TD>0.632457</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Shrew sorAra1</TH>
  <TD>262057</TD>
  <TD>2936 Mb</TD>
  <TD>0.658734</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Tenrec echTel1</TH>
  <TD>325491</TD>
  <TD>3823 Mb</TD>
  <TD>0.666303</TD>
  <TD>3000</TD>
  <TD>medium</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Opossum monDom4</TH>
  <TD>9</TD>
  <TD>3431 Mb</TD>
  <TD>0.909852</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Platypus ornAna1</TH>
  <TD>201522</TD>
  <TD>1996 Mb</TD>
  <TD>1.165888</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Chicken galGal3</TH>
  <TD>33</TD>
  <TD>1032 Mb</TD>
  <TD>1.285399</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Lizard anoCar1</TH>
  <TD>7233</TD>
  <TD>1781 Mb</TD>
  <TD>1.404225</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>X. tropicalis xenTro2</TH>
  <TD>19759</TD>
  <TD>1513 Mb</TD>
  <TD>1.726205</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Stickleback gasAcu1</TH>
  <TD>21</TD>
  <TD>400 Mb</TD>
  <TD>2.012649</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Zebrafish danRer4</TH>
  <TD>25</TD>
  <TD>1547 Mb</TD>
  <TD>2.027153</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Tetraodon tetNig1</TH>
  <TD>21</TD>
  <TD>217 Mb</TD>
  <TD>2.051015</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Fugu fr2</TH>
  <TD>1</TD>
  <TD>400 Mb</TD>
  <TD>2.086669</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>xx.123</TD>
  <TD>xx.456</TD>
  <TD>tbd</TD>
</TR>

<TR>
  <TH>Medaka oryLat1</TH>
  <TD>24</TD>
  <TD>724 Mb</TD>
  <TD>2.200402</TD>
  <TD>5000</TD>
  <TD>loose</TD>
  <TD>1.933</TD>
  <TD>6.495</TD>
  <TD>2007-08-31</TD>
</TR>

</TABLE>


(*) chrom count does not include haplotypes, chr*_random, chrUn or chrM unless chrUn or scaffolds are the only sequences for that assembly.

The genome size has the same limitation as the chrom count, no randoms.

Tree distances are from the hg18 28-way measurements, with ponAbe1 and calJac1 manually inserted into the tree.

==blastz alignment parameters details==

One special run, Rat rn4:
<PRE>
M=40M, K=4500, L=4500, Y=15000, T=2 O=600, Q=mouse_rat.q E=55
</PRE>

<TABLE BORDER=1>
<TR>
  <TH>query </TH>
  <TD>abridged<BR>repeats</TD>
  <TD>M</TD>
  <TD>K</TD>
  <TD>L</TD>
  <TD>Q</TD>
  <TD>Y</TD>
</TR>
<TR>
  <TH>Rat rn4</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>4500</TD>
  <TD>4500</TD>
  <TD>mouse-rat</TD>
  <TD>15000</TD>
</TR>
<TR>
  <TH>Human hg18</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Rhesus rheMac2</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Orangutan ponAbe1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Marmoset calJac1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Chimp panTro2</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>GuineaPig cavPor2</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Horse equCab1</TH>
  <TD>no</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>TreeShrew tupBel1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Bushbaby otoGar1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Armadillo dasNov1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Rabbit oryCun1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Cat felCat3</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Dog canFam2</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Elephant loxAfr1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Cow bosTau3</TH>
  <TD>no</TD>
  <TD>40M</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Hedgehog eriEur1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Shrew sorAra1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Tenrec echTel1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>3K</TD>
  <TD>3K</TD>
  <TD>default</TD>
  <TD>9400</TD>
</TR>
<TR>
  <TH>Opossum monDom4</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Platypus ornAna1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Chicken galGal3</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Lizard anoCar1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>X_tropicalis xenTro2</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Stickleback gasAcu1</TH>
  <TD>no</TD>
  <TD>40M</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Zebrafish danRer4</TH>
  <TD>yes</TD>
  <TD>40M</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Tetraodon tetNig1</TH>
  <TD>no</TD>
  <TD>40M</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Fugu fr2</TH>
  <TD>no</TD>
  <TD>40M</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
<TR>
  <TH>Medaka oryLat1</TH>
  <TD>no</TD>
  <TD>50</TD>
  <TD>2200</TD>
  <TD>6000</TD>
  <TD>HoxD55</TD>
  <TD>3400</TD>
</TR>
</TABLE>

==default blastz parameters==
<PRE>
m=80  v=0  B=2  C=0  E=30  G=0  H=0  K=3000 L=K
M=0 O=400 P=1 R=0 T=1 W=8 X=10*(A-to-A match score)
Y=O+300*E Z=1

From the blastz usage message:

Default values are given in parentheses.
  m(80M) bytes of space for trace-back information
  v(0) 0: quiet; 1: verbose progress reports to stderr
  B(2) 0: single strand; >0: both strands
  C(0) 0: no chaining; 1: just output chain; 2: chain and extend;
       3: just output HSPs
  E(30) gap-extension penalty.
  G(0) diagonal chaining penalty.
  H(0) interpolate between alignments at threshold K = argument.
  K(3000) threshold for MSPs
  L(K) threshold for gapped alignments
  M(0) mask any base in seq1 hit this many times; 0 = no dynamic masking
  O(400) gap-open penalty.
  P(1) 0: entropy not used; 1: entropy used; >1 entropy with feedback.
  Q load the scoring matrix from a file.
  R(0) antidiagonal chaining penalty.
  T(1) 0: W-bp words;  1: 12of19;  2: 12of19 without transitions.
                       3: 14of22;  4: 14of22 without transitions.
  W(8) word size (unused unless T=0)
  X(10*(A-to-A match score)) X-drop parameter for ungapped extension.
  Y(O+300E) X-drop parameter for gapped extension.
  Z(1) increment between successive words in sequence 1.
</PRE>

<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The mouse-rat<BR>scoring matrix is:</TD></TR>

<TR><TD>
<TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
<TR><TH>G</TH><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>
<TR><TH>T</TH><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>56</TD><TD>-109</TD><TD>-45</TD><TD>-137</TD></TR>
<TR><TH>C</TH><TD>-109</TD><TD>100</TD><TD>-103</TD><TD>-45</TD></TR>
<TR><TH>G</TH><TD>-45</TD><TD>-103</TD><TD>100</TD><TD>-109</TD></TR>
<TR><TH>T</TH><TD>-137</TD><TD>-45</TD><TD>-109</TD><TD>56</TD></TR>
</TABLE>
O=600 E=55
</TD>
</TR></TABLE>

==axtChain matrix parameters==
The "medium" gap score matrix, tuned for the mouse-human distance is:

<PRE>
tableSize    11
smallSize   111
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300
</PRE>

The "loose" gap score matrix, tuned for the chicken-human distance is:

<PRE>
tablesize    11
smallSize   111
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000
</PRE>

==the tree diagram==

<PRE>
((((((((

 (((Mouse_mm9:0.076274,Rat_rn4:0.084383):0.200607,
    GuineaPig_cavPor2:0.202990):0.034350,
        Rabbit_oryCun1:0.208548):0.014587,

((((((Human_hg18:0.005873,Chimp_panTro2:0.007668):0.013037,
   Orangutan_ponAbe1:0.02):0.013037,Rhesus_rheMac2:0.031973):0.0365,
        Marmoset_calJac1:0.07):0.0365,Bushbaby_otoGar1:0.151185):0.015682,
           TreeShrew_tupBel1:0.162844):0.006272):0.019763,

 ((Shrew_sorAra1:0.248532,Hedgehog_eriEur1:0.222255):0.045693,

 (((Dog_canFam2:0.101137,Cat_felCat3:0.098203):0.048213,
    Horse_equCab1:0.099323):0.007287,
        Cow_bosTau3:0.163945):0.012398):0.018928):0.030081,

 (Armadillo_dasNov1:0.133274,(Elephant_loxAfr1:0.103030,
        Tenrec_echTel1:0.232706):0.049511):0.008424):0.213469,

 Opossum_monDom4:0.320721):0.088647,
    Platypus_ornAna1:0.488110):0.118797,
        (Chicken_galGal3:0.395136,Lizard_anoCar1:0.513962):0.093688):0.151358,
            Frog_xenTro2:0.778272):0.174596,

 (((Tetraodon_tetNig1:0.203933,Fugu_fr2:0.239587):0.203949,
    (Stickleback_gasAcu1:0.314162,Medaka_oryLat1:0.501915):0.055354):0.346008,
Zebrafish_danRer4:0.730028):0.174596);
</PRE>