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请教有关phylogenetic tree

请教有关phylogenetic tree# Biology - 生物学

q*n2013-02-24 08:02

1 楼

虽然是周六，但是好像事儿比平时还多......亲，你们有这种感受吗？
到家已是不早了，做米饭啥的有点来不及，小盆友们说他们的肚子有点急哈！
好吧！来个快滴～干炒牛河！
（记得刚来美国的时候，在粤菜馆看到这道菜的第一反应竟是,啊？河马也可以炒着吃
啊？！@#￥%……&×（×&%……￥#@！@#￥%……&×嘻嘻～当时怎么也没想到竟然是
种米粉！哈哈～～）
干炒牛河，我的做法：
牛排肉切片，料酒，盐，芡粉，抓匀。
雪豆，胡萝卜飞水。（平时不加雪豆的，今儿那个蔬菜部的李师傅竟然给了我九毛一磅
的价格.......我一听乐极了，说来两磅，不行，你得买一箱，十磅！@#￥%……&×（
）（×&……%￥#￥% 晕了！好在我爱吃豆豆 :-)
热锅，上油，炒牛肉8成熟，放入一勺蒜蓉，姜片，蚝油，豆芽，雪豆，胡萝卜，炒匀
，最后放入微波热过切成条的河粉，九层塔，炒匀，均色就好了啦！

d*o2013-02-24 08:02

2 楼

老大很喜欢吃苹果，想带苹果在学校吃。
现在是换牙期，没法儿吃整个的苹果，要我切成小块。
但是切块的苹果很容易就变黄了，没法带到学校。
老大很不满意，说：“为什么麦当劳的苹果就能装在塑料袋里？”
大家有什么主意？
谢谢。

y*n2013-02-24 08:02

3 楼

请问iphone6使用hangouts时的incoming call能否能bypass指纹识别或锁屏密码？
一般的incoming call自动bypass指纹识别或者锁屏密码，这样就方便了接听。但是
hangouts的incoming call总要指纹识别一下或者输入锁屏密码，这样很耽误事，有办
法不要指纹识别或输入密码吗？
刚试了下安卓，hangouts的incoming call和普通电话一样，不需要密码验证直接接听

c*y2013-02-24 08:02

4 楼

都是peptide sequences,分别试了neighbour joining, maximum likelihood, 还有
bayesian inference. 发现出来的结果完全是不一样的. 本人不是学进化的,只是在这
种情况下, 应该选哪个呢?为什么?

c*e2013-02-24 08:02

5 楼

这个好吃，大学的时候吃了很多。

【在 q**********n 的大作中提到】

: 虽然是周六，但是好像事儿比平时还多......亲，你们有这种感受吗？
: 到家已是不早了，做米饭啥的有点来不及，小盆友们说他们的肚子有点急哈！
: 好吧！来个快滴～干炒牛河！
: （记得刚来美国的时候，在粤菜馆看到这道菜的第一反应竟是,啊？河马也可以炒着吃
: 啊？！@#￥%……&×（×&%……￥#@！@#￥%……&×嘻嘻～当时怎么也没想到竟然是
: 种米粉！哈哈～～）
: 干炒牛河，我的做法：
: 牛排肉切片，料酒，盐，芡粉，抓匀。
: 雪豆，胡萝卜飞水。（平时不加雪豆的，今儿那个蔬菜部的李师傅竟然给了我九毛一磅
: 的价格.......我一听乐极了，说来两磅，不行，你得买一箱，十磅！@#￥%……&×（

s*l2013-02-24 08:02

6 楼

用柠檬水泡一下。

【在 d****o 的大作中提到】

: 老大很喜欢吃苹果，想带苹果在学校吃。
: 现在是换牙期，没法儿吃整个的苹果，要我切成小块。
: 但是切块的苹果很容易就变黄了，没法带到学校。
: 老大很不满意，说：“为什么麦当劳的苹果就能装在塑料袋里？”
: 大家有什么主意？
: 谢谢。

H*g2013-02-24 08:02

7 楼

I am not studying evolutionary biology neither. Just my 2cents. I guess I
would forget the neighbor-joining method.
Assuming that you have a good alignment with the most biological sense (
functional domain well aligned), good bootstrap value for ML and good
convergence for Bayesian Inference, regarding of the trees that are
generated from those different methods, you may have to distinguish them by
yourself by figuring out which one makes the most biological sense.
Without a thorough look at the trees, I tend to like the one by Bayesian
Inference, again assuming that you have a good alignment and a good
convergence..

a*n2013-02-24 08:02

8 楼

颜色漂亮，但就不像正宗的干炒牛河了，我吃了这么多年，一般就是豆芽、洋葱和一点
青葱，牛河要干爽一点

r*f2013-02-24 08:02

9 楼

嗯,mcD的苹果很酸

【在 s***l 的大作中提到】

: 用柠檬水泡一下。

N*n2013-02-24 08:02

10 楼

what software does you use?

【在 c***y 的大作中提到】

: 都是peptide sequences,分别试了neighbour joining, maximum likelihood, 还有
: bayesian inference. 发现出来的结果完全是不一样的. 本人不是学进化的,只是在这
: 种情况下, 应该选哪个呢?为什么?

c*n2013-02-24 08:02

11 楼

呵呵，看着就想吃

d*o2013-02-24 08:02

12 楼

多谢。

【在 s***l 的大作中提到】

: 用柠檬水泡一下。

c*y2013-02-24 08:02

13 楼

My alignment came from clustalw
Bootstrapping NJ tree was generated using clustalx (100 bootstraps); ML tree
was generated using phylip package with PAM model; and BI tree was
generated using MrBayes...
Does software matter?

【在 N******n 的大作中提到】

: what software does you use?

F*Y2013-02-24 08:02

14 楼

非常喜欢吃这个

d*o2013-02-24 08:02

15 楼

他从小爱吃酸苹果，呵呵。

【在 r*f 的大作中提到】

: 嗯,mcD的苹果很酸

j*e2013-02-24 08:02

16 楼

what's the bootstrapping scores for the three trees?

tree

【在 c***y 的大作中提到】

: My alignment came from clustalw
: Bootstrapping NJ tree was generated using clustalx (100 bootstraps); ML tree
: was generated using phylip package with PAM model; and BI tree was
: generated using MrBayes...
: Does software matter?

w*42013-02-24 08:02

17 楼

晒昵称

n*h2013-02-24 08:02

18 楼

切之前, 用盐水泡苹果

【在 d****o 的大作中提到】

N*n2013-02-24 08:02

19 楼

ML has a better statistical property,and inference the model parameter
statistically, but is very time consuming comparing to NJ.
Bayesian inference is become popular because of computational power
advancement. it considers the prior and the parameter together.
Only 2 cents from statistical perspective, not familiar with evolution.

【在 c***y 的大作中提到】

i*92013-02-24 08:02

20 楼

re这个。蔡澜品味里面介绍的最好吃的干炒牛河就是只有你说的料。

【在 a********n 的大作中提到】

: 颜色漂亮，但就不像正宗的干炒牛河了，我吃了这么多年，一般就是豆芽、洋葱和一点
: 青葱，牛河要干爽一点

r*f2013-02-24 08:02

21 楼

葱白~~~~~~~~~~~~~ 那就一切没问题了，哈哈

【在 d****o 的大作中提到】

: 他从小爱吃酸苹果，呵呵。

c*y2013-02-24 08:02

22 楼

first need to correct some typo: bootstrapping NJ tree from 1000 bootstraps
instead of 100.
My running shows that BI tree takes longer time, 2 days; whereas ML tree
took less than 8 hrs.

【在 N******n 的大作中提到】

: ML has a better statistical property,and inference the model parameter
: statistically, but is very time consuming comparing to NJ.
: Bayesian inference is become popular because of computational power
: advancement. it considers the prior and the parameter together.
: Only 2 cents from statistical perspective, not familiar with evolution.

u*s2013-02-24 08:02

23 楼

很不错哦~

【在 q**********n 的大作中提到】

d*o2013-02-24 08:02

24 楼

？？把苹果连皮泡盐水里，然后再切？很诡异

【在 n********h 的大作中提到】

: 切之前, 用盐水泡苹果

c*y2013-02-24 08:02

25 楼

how do I check the convergence for BI tree?

by

【在 H*g 的大作中提到】

: I am not studying evolutionary biology neither. Just my 2cents. I guess I
: would forget the neighbor-joining method.
: Assuming that you have a good alignment with the most biological sense (
: functional domain well aligned), good bootstrap value for ML and good
: convergence for Bayesian Inference, regarding of the trees that are
: generated from those different methods, you may have to distinguish them by
: yourself by figuring out which one makes the most biological sense.
: Without a thorough look at the trees, I tend to like the one by Bayesian
: Inference, again assuming that you have a good alignment and a good
: convergence..

c*y2013-02-24 08:02

26 楼

河马是什么？
外相有点不正宗，应该加点老抽

【在 q**********n 的大作中提到】

d*o2013-02-24 08:02

27 楼

哈，他做baby的时候，我就发现，甜苹果打的泥他不喜欢，酸苹果的就很爱。
害得我满大街找酸苹果:D

【在 r*f 的大作中提到】

: 葱白~~~~~~~~~~~~~ 那就一切没问题了，哈哈

N*n2013-02-24 08:02

28 楼

the usual Bayesian approach obtains the posterior probability through MCMC
sampling and takes longer time. ML gets its parameter estimation through
numerical optimization and therefore, faster than BI.

bootstraps

【在 c***y 的大作中提到】

: first need to correct some typo: bootstrapping NJ tree from 1000 bootstraps
: instead of 100.
: My running shows that BI tree takes longer time, 2 days; whereas ML tree
: took less than 8 hrs.

R*s2013-02-24 08:02

29 楼

【在 c******y 的大作中提到】

: 河马是什么？
: 外相有点不正宗，应该加点老抽

w*t2013-02-24 08:02

30 楼

酸苹果满大街都是啊，我家只吃甜水果的才苦了
草莓西红柿都不吃，就爱西瓜，葡萄

【在 d****o 的大作中提到】

: 哈，他做baby的时候，我就发现，甜苹果打的泥他不喜欢，酸苹果的就很爱。
: 害得我满大街找酸苹果:D

l*12013-02-24 08:02

31 楼

plus one article:
Algorithms Mol Biol. 2010 5:35.
Estimating the evidence of selection and the reliability of inference in
unigenic evolution.
by Fernandes AD et al,
HTTP: //www.ncbi.nlm.nih.gov/pubmed/21059250
and one Book
by Robert CP: The Bayesian choice: from decision-theoretic foundations to
computational implementation. 2 edition. Springer texts in statistics, New
York: Springer; 2001.
free down link:
HTTP: //ishare.iask.sina.com.cn/f/15300682.html

d*o2013-02-24 08:02

32 楼

酸苹果可不多，只有granny smith这一种。

【在 w********t 的大作中提到】

: 酸苹果满大街都是啊，我家只吃甜水果的才苦了
: 草莓西红柿都不吃，就爱西瓜，葡萄

H*g2013-02-24 08:02

33 楼

For the convergence of Bayesian Inference tree, you could go to the .log
file, check the value behind the last "Average standard deviation of split
frequencies:". Without the info of this value at least, we would not know if
we have set the generation number or the probe temperature correctly, not
saying the resulted tree is appropriate for downstream analysis.
A good and biological meaningful alignment is essential for the analysis.
Make sure of this before jumping into the actual analysis. This means, if we
use the resulted alignment from ClustalW/MAFFT/T-COFFEE without any manual
adjustment, or if we haven't carefully examined the alignment from head to
toe, it is almost certain that the alignment is not ideal and the resulted
tree is destined to be inaccurate. Similarly, if we haven't compared the
alignment results from multiple alignment programs with different algorithms
, probably we haven't done enough homework to understand some basic concepts
at least, and are not ready to perform the analysis yet.
For the computation power, try an on-campus cluster or the free public
cluster CIPRES http://www.phylo.org/index.php/portal/. CIPRES has multiple built-in phylogenetic tools, including sequence alignment tools (e.g., CLustalX/MAFFT) and phylogenetic tree inference tools (e.g., RAxML and MrBayes).
I am not majored in phylogenetics. Just 2 cents.

【在 c***y 的大作中提到】

: how do I check the convergence for BI tree?
:
: by

w*t2013-02-24 08:02

34 楼

超市里卖的切好了的小包装袋的苹果，全是酸的

【在 d****o 的大作中提到】

: 酸苹果可不多，只有granny smith这一种。

c*y2013-02-24 08:02

35 楼

Thank you very much for your explanation. I am reading some relevant book
now, slowly though.
I checked my log file and got the following informatuiion:
Average standard deviation of split frequencies = 0.075483
Maximum standard deviation of split frequencies = 0.345682
Is it good or not?
Many articles mentioned manual adjustment after alignment. Does it mean I
just visually check and then do the adjustment? It sounds very time-
consuming and hard to be error-free since I have about 100 sequences and 900
aa in length...

if
we
manual

【在 H*g 的大作中提到】

: For the convergence of Bayesian Inference tree, you could go to the .log
: file, check the value behind the last "Average standard deviation of split
: frequencies:". Without the info of this value at least, we would not know if
: we have set the generation number or the probe temperature correctly, not
: saying the resulted tree is appropriate for downstream analysis.
: A good and biological meaningful alignment is essential for the analysis.
: Make sure of this before jumping into the actual analysis. This means, if we
: use the resulted alignment from ClustalW/MAFFT/T-COFFEE without any manual
: adjustment, or if we haven't carefully examined the alignment from head to
: toe, it is almost certain that the alignment is not ideal and the resulted

k*n2013-02-24 08:02

36 楼

这是一般用来做派的阿,我以前也喜欢吃

【在 d****o 的大作中提到】

: 酸苹果可不多，只有granny smith这一种。

D*R2013-02-24 08:02

37 楼

我家是切成小块后，泡淡盐水，最后苹果还有点淡淡的咸味，不难吃。
我以前也切过莲花状的，不掰开放着，也能一定程度保鲜，到时候掰开吃，适用于小苹
果。。。

r*y2013-02-24 08:02

38 楼

我是泡盐水的，还是会黄。

★ 发自iPhone App: ChineseWeb - 中文网站浏览器

【在 D**********R 的大作中提到】

: 我家是切成小块后，泡淡盐水，最后苹果还有点淡淡的咸味，不难吃。
: 我以前也切过莲花状的，不掰开放着，也能一定程度保鲜，到时候掰开吃，适用于小苹
: 果。。。

D*R2013-02-24 08:02

39 楼

试试整个都浸泡，你是一直泡着，放密封塑料饭盒的吗？或者多加些盐？我家都是这么
处理，也许有点微微变色，我都看不出区别来，但是肯定比不泡要好。
说实话，给他切了削了已经不容易了，如果我娃因为这个挑剔，我就干脆不给苹果。他
如果真想吃，就不必在意这个。

【在 r**y 的大作中提到】

: 我是泡盐水的，还是会黄。
:
: ★ 发自iPhone App: ChineseWeb - 中文网站浏览器

m*k2013-02-24 08:02

40 楼

http://www.wikihow.com/Keep-a-Cut-Apple-from-Turning-Brown
1)Choose apples that are less prone to browning. A study found that Arangeh
tend to brown the least. Granny Smith and Golden Smoty apples also showed
minimal browning. Golden Delicious apples were in the middle, and Red
Delicious apples browned the most
2)Cut the apple underwater. This keeps the enzyme from making contact with
oxygen. Keep the cut apple in the water until ready to serve.
3)Coat the exposed flesh in acid. By bringing the pH below 2, the enzyme
that makes the apple flesh turn brown is deactivated.[3] Here are some acids
you can use:
Ascorbic acid, better known as vitamin C. Look for it in the canning section
or pharmacy as powder. Apply directly or dissolved in water (1/2 tsp. per 2
1/2 cups of water[4]).
Lemon or lime juice. It's not as effective as ascorbic acid, but it'll do in
a pinch, and they're more readily available. The juice can be diluted up to
3:1. Lemon juice will have a less obvious taste than lime juice.
Use Ginger ale. Soak in ginger ale for 10 min and then eat or you can put
them in a bag for a picnic.
4)Blanch the apples. This will denature the enzyme. Let the apple sit in
boiling water for one or two minutes, then rinse with cold water. They can
then be eaten, frozen, or used for apple pie.
5)Cover exposed apple flesh tightly in plastic wrap. This will work best if
you have half an apple (as opposed to several pieces). Try to avoid having
creases in the plastic wrap on the exposed side. This technique keeps the
air away from the apple flesh to prevent the apple flesh from oxidizing
6) Soak apple pieces in a slightly salty water solution for a few seconds.
Remove and enjoy white apple pieces for a considerable time. Works well if
you're adding apples to a fruit salad.
7)Another thing to do is to pour a tablespoon of lemon juice over the apple
slice and you can either put it into the refrigerator or you can keep it at
room temperature.

k*y2013-02-24 08:02

41 楼

直接买超市里切好的苹果。Costco一大包，够吃一个星期的了。也不贵，还省事。

r*f2013-02-24 08:02

42 楼

太复杂了,吃苹果干吧

Arangeh
acids

【在 m**k 的大作中提到】

: http://www.wikihow.com/Keep-a-Cut-Apple-from-Turning-Brown
: 1)Choose apples that are less prone to browning. A study found that Arangeh
: tend to brown the least. Granny Smith and Golden Smoty apples also showed
: minimal browning. Golden Delicious apples were in the middle, and Red
: Delicious apples browned the most
: 2)Cut the apple underwater. This keeps the enzyme from making contact with
: oxygen. Keep the cut apple in the water until ready to serve.
: 3)Coat the exposed flesh in acid. By bringing the pH below 2, the enzyme
: that makes the apple flesh turn brown is deactivated.[3] Here are some acids
: you can use:

d*o2013-02-24 08:02

43 楼

感觉不新鲜，而且冰箱压力大

【在 k**y 的大作中提到】

: 直接买超市里切好的苹果。Costco一大包，够吃一个星期的了。也不贵，还省事。

d*o2013-02-24 08:02

44 楼

嗯，学习了，2步
1，不买红苹果，反正我们也不爱吃，嘿嘿
2，少让苹果接触氧气/洒酸汁/煮熟
好像煮一下比较简单，明天我试试。

Arangeh
acids

【在 m**k 的大作中提到】

h*m2013-02-24 08:02

45 楼

给娃切好放塑料饭盒里就再也不管它黄了还是黑了的后妈飘过。。。

m*k2013-02-24 08:02

46 楼

我觉得抹柠檬更简单。煮过的味道不同啊。也麻烦些

【在 d****o 的大作中提到】

: 嗯，学习了，2步
: 1，不买红苹果，反正我们也不爱吃，嘿嘿
: 2，少让苹果接触氧气/洒酸汁/煮熟
: 好像煮一下比较简单，明天我试试。
:
: Arangeh
: acids

z*92013-02-24 08:02

47 楼

把苹果去皮切成您想要的形状，用1小勺盐放在凉开水里溶解，放入切好的苹果粒浸泡
10分钟，然后装入食品密封袋就可以了。有的说用盐水浸泡还有黄色那是不够时间浸泡
。

l*n2013-02-24 08:02

48 楼

原来是这样！我家娃也爱西瓜，葡萄，不爱草莓西红柿，我都不明白为什么。
他还发明了一个国家，叫西瓜牙，为了和葡萄牙般配。也怪我讲了那个笑话：有两颗牙
，一颗葡萄牙，一颗西班牙。

【在 w********t 的大作中提到】

: 酸苹果满大街都是啊，我家只吃甜水果的才苦了
: 草莓西红柿都不吃，就爱西瓜，葡萄

m*22013-02-24 08:02

49 楼

lemon juice.

【在 d****o 的大作中提到】