y*****n
发帖数: 45 | 1 请教大家一个问题：在建phylogenetic tree的时候，有没有什么情况下rooting是不重
要的或者不可能
rooting的？ |
v***r
发帖数: 1046 | 2 By assuming constant rate 或者有out-group的时候，可以确定root.
【在 y*****n 的大作中提到】
: 请教大家一个问题：在建phylogenetic tree的时候，有没有什么情况下rooting是不重
: 要的或者不可能
: rooting的？
|
y*****n
发帖数: 45 | 3 我的意思不是怎样可以确定根啊，朋友看清楚我问题啊。 |
v***r
发帖数: 1046 | 4 "有没有什么情况下rooting是不重要的"
~~~~~没觉的rooting重要. 你的具体问题是什么，提出来好讨论。
"或者不可能rooting的？"
~~~~~除了我说的情况，不就是不能rooting的??
【在 y*****n 的大作中提到】
: 我的意思不是怎样可以确定根啊，朋友看清楚我问题啊。
|
l**********1
发帖数: 5204 | 5 TDRL tandem duplication and random loss and or Horizon transfer event,
pls refer
>Thus, for any given tandem duplication history, Fitch (1977) and Elemento
et al. (2002) defined a corresponding rooted duplication >tree (RDT) in
which nonnested duplication events are not temporally >related and an (
unrooted) du- plication tree (DT) in which the >root location is also lost.
>HTTP double dot//hal.archives-ouvertes.fr/docs/00/19/19/24/PDF/D109.PDF
or 2012 one PhD dissertation from National University of Ireland
>HTTP double dot //eprints.nuim.ie/4517/1/SineadHamiltonPhDThesis2012.pdf
【在 y*****n 的大作中提到】
: 我的意思不是怎样可以确定根啊，朋友看清楚我问题啊。
|
y*****n
发帖数: 45 | |
l**********1
发帖数: 5204 | 7 plus
The General Time Reversible model (GTR) (Waddell and Steel 1997)
can be applied to unrooted trees from it allows base composition and
substitution rates to vary but the rate of change from A to B must equal the
rate of change from B to A.
from that 2012 PhD dissertation:
>HTTP double dot //eprints.nuim.ie/4517/1/SineadHamiltonPhDThesis2012.pdf
its pp 33
cited
>1.3.4 Choosing a Matrix Model
pp34
>often does not fit the data very well (Keane et al. 2004). The Jukes and
>Cantor model (JC69) assumes equal base frequencies as well as equal rates
of
change between bases. The Kimura 2-Parameter model (K2P) (Kimura and Ohta
1972) improves on this by allowing different substitution rates for
transitions and transversions.
below omitted
The General Time Reversible model (GTR) (Waddell and Steel 1997) allows base
composition and
substitution rates to vary but the rate of change from A to B must equal the
rate of change from B to A. This means that this model is reversible and
can be applied to unrooted trees.
or
pp137
Figure 3.6: (b) the same topology unrooted. Although the support for some
of the clades are high, this tree shows a very unlikely topology where Gt2
is the outgroup to the Gt1 and Gt3 clades. The support for the Gt1 and Gt3
clade is extremely low. This is most likely to be caused by a rooting
problem. If the outgroup is ignored in this tree and the tree is considered
unrooted, then the lamprey long sequence (Gt2) is adjacent to the Gt2
sequences, as would be expected if the lamprey long sequence was a member of
cone type Transducins clade, Gt2.
bla bla ba
that Fig. 3.6 (b) attached here too.
【在 y*****n 的大作中提到】
: 谢谢各位高人解惑啊
|
