The tree I made is showing incorrect and very variable topologies with low bootstrap value with one protein sequence. But when I made the tree of the same taxa with another protein sequence, it shows high bootstrap values and more consistent topologies.
So, how does the sequence influence the tree structure? Does any limitation of maximum parsimony method explain these results?
TLDR; What do the numbers beside the branches of a Maximum parsimony tree mean?
Hello! I'm using the bootstrap method with 1000 replicates with Tree Bisection Reconnection (TBR)
I'd like to know what these numbers beside the branches signify. I thought it would be the number of changes or the bootstrap values.
https://preview.redd.it/81q1q0mjjzu31.png?width=402&format=png&auto=webp&s=12fdd6e4fda2138a9dcb4216aba6313e551213a7
This is just a small part of the tree and it would be quite lengthy if I added the rest as the tree has 100 sequences in it. Also, I'm a STEM student in the 11th grade, just putting it out there so you can gauge my expertise on Bioinformatics, as it was just introduced to us recently.
Cheers in advance!
TL;DR: What's the point of doing research in Maximum Parsimony based methods for phylogeny construction if the Maximum Likelihood based methods became the standard for some time and, as far as I know, yield much better and consistent results? Are there situations where Maximum Parsimony based methods are better? What's the point of doing research on rearrangement events in isolation when there are more robust models? What's the biological relevance? Could you point me to some papers that make comparisons, give a broad range of applications of each method, etc?
Hey, so I'm an undergrad in computer science writing a dissertation about the DCJ (Double Cut and Join) Median Problem.
For those who don't know, the DCJ is a model to represent various rearrangements operations (reversals, transpositions, etc) in a genome. It's a robust model to calculate the edit distance between two genomes, but as far as I know, it doesn't include indels and duplicate genes, although there are papers that try to achieve this. So, here is the problem statement: given genomes A, B and C, find a 4th genome D such that d(A,D) + d(B,D) + d(C,D) is minimized, where d is the DCJ distance between two given genomes. It's known that this problem is NP-Hard, so the algorithms to solve it are approximate, heuristics, and so on.
You may have noticed by now that this problem falls under the umbrella of Maximum Parsimony based methods. I wanted to give you a brief overview so you could see the big picture. I have been doing some bibliographical research to start my dissertation, but after I came across broader papers and talked to some biologist colleagues, it seems that Maximum Likelihood based methods are the standard in phylogenetics. Colleagues on the lab I work on use programs like MrBayes and RAxML in a daily basis. What I could read by now is that these methods are more consistent, realistic, etc.
So I started to ponder, what's the point of doing research on Maximum Parsimony based methods at all? What are the advantages? Are they worth it? I have seen many papers that treat some rearrangement events in isolation, like sorting by reversals, sorting by transpositions, etc. Why do research in these events in isolation if there are models like the DCJ and others (HP, SCJ, etc)? What's the biological relevance? Could you point me to some papers that make comparisons, show where one can be used over the other, etc? Sorry if this is a naive question (it probably is), but I'
... keep reading on reddit ➡I met an exercise like this:
We want to apply an affine gap penalty model in the maximum parsimony model. We propose to apply the Fitch algorithm to compute the ancestral sequences first, and then to use these ancestral sequences to score the alignment using the affine gap penalty model. Explain why this algorithm is not optimal.
As far as I can see, to apply Finch's algorithm, we need a fixed phylogeny tree and a multiple alignment, then we can infer ancestral nodes. But I don't quite get what "use these ancestral sequences to score the alignment..."
What do you think?
BTW: Is there any online forum or mail list that people discuss computational biology questions?
I don't want to step on anybody's toes here, but the amount of non-dad jokes here in this subreddit really annoys me. First of all, dad jokes CAN be NSFW, it clearly says so in the sub rules. Secondly, it doesn't automatically make it a dad joke if it's from a conversation between you and your child. Most importantly, the jokes that your CHILDREN tell YOU are not dad jokes. The point of a dad joke is that it's so cheesy only a dad who's trying to be funny would make such a joke. That's it. They are stupid plays on words, lame puns and so on. There has to be a clever pun or wordplay for it to be considered a dad joke.
Again, to all the fellow dads, I apologise if I'm sounding too harsh. But I just needed to get it off my chest.
Alot of great jokes get posted here! However just because you have a joke, doesn't mean it's a dad joke.
THIS IS NOT ABOUT NSFW, THIS IS ABOUT LONG JOKES, BLONDE JOKES, SEXUAL JOKES, KNOCK KNOCK JOKES, POLITICAL JOKES, ETC BEING POSTED IN A DAD JOKE SUB
Try telling these sexual jokes that get posted here, to your kid and see how your spouse likes it.. if that goes well, Try telling one of your friends kid about your sex life being like Coca cola, first it was normal, than light and now zero , and see if the parents are OK with you telling their kid the "dad joke"
I'm not even referencing the NSFW, I'm saying Dad jokes are corny, and sometimes painful, not sexual
So check out r/jokes for all types of jokes
r/unclejokes for dirty jokes
r/3amjokes for real weird and alot of OC
r/cleandadjokes If your really sick of seeing not dad jokes in r/dadjokes
Punchline !
Edit: this is not a post about NSFW , This is about jokes, knock knock jokes, blonde jokes, political jokes etc being posted in a dad joke sub
Edit 2: don't touch the thermostat
Do your worst!
How the hell am I suppose to know when it’s raining in Sweden?
Ants don’t even have the concept fathers, let alone a good dad joke. Keep r/ants out of my r/dadjokes.
But no, seriously. I understand rule 7 is great to have intelligent discussion, but sometimes it feels like 1 in 10 posts here is someone getting upset about the jokes on this sub. Let the mods deal with it, they regulate the sub.
They were cooked in Greece.
I'm surprised it hasn't decade.
Now that I listen to albums, I hardly ever leave the house.
Don't you know a good pun is its own reword?
Two muffins are in an oven, one muffin looks at the other and says "is it just me, or is it hot in here?"
Then the other muffin says "AHH, TALKING MUFFIN!!!"
For context I'm a Refuse Driver (Garbage man) & today I was on food waste. After I'd tipped I was checking the wagon for any defects when I spotted a lone pea balanced on the lifts.
I said "hey look, an escaPEA"
No one near me but it didn't half make me laugh for a good hour or so!
Edit: I can't believe how much this has blown up. Thank you everyone I've had a blast reading through the replies 😂
It really does, I swear!
And now I’m cannelloni
Because she wanted to see the task manager.
But that’s comparing apples to oranges
And boy are my arms legs.
I was recently watching a college lecture where the professor prefaced a discussion of game theory with "and the concept of a prisoner's dilemma is one of those things I am confident saying you are not an educated person in any meaningful sense if you have never taken the trouble to understand or learn it. The idea that we can map out the conditions under which cooperators will defect given individual incentives, even despite the fact that the collective incentive can be to cooperate for a higher payoff, is so fundamental to understanding the problems of the 21st century (like Climate Change) that I think it's only fair that we set our bar/expectations for the educated person high enough that they would know this enough to be able to act on it."
This got me thinking: what is your list (or solitary individual entry for what could become a larger list) of things every 21st Century person who likes to think of themselves as having achieved a serious education should know, but probably doesn't? I say "probably doesn't" because a list of what an educated person should know in general would be too long and (for the most part) too obvious for my purposes here (i.e. please don't say something like "the earth orbits the sun"). I also want people to emphasize knowing things that are considered groundbreaking in their respective fields and that may even have a practical or important connection to a larger issue, particularly the larger issues that we will be counting on the "educated (but common) person" to address in this century.
Pick any discipline you want, but try to meet my criteria. Here's mine! (A list like this is bound to sound opinionated and self-congratulatory because it's an attempt to list the things you think you already know but that many others don't, but for the same reason that the "rationalist" community has chosen a vaguely positive adjective for itself, and only aspirationally rather than narcissistically, I want you to put aside the self-conscious worry that you sound self-indulgent and just do your best to outline the greatest ideas an education can impart for someone aspiring to a true education)
These are not in any particular order from most to least important, but more "what occurred to me first," and it is bound to be horribly incomplete or include things it shouldn't--that's where you come in!
Here goes nothing:
- Graham Oppy's concept of rational belief-formation as a process of "worldview comparison" where people follow the
Heard they've been doing some shady business.
but then I remembered it was ground this morning.
Edit: Thank you guys for the awards, they're much nicer than the cardboard sleeve I've been using and reassures me that my jokes aren't stale
Edit 2: I have already been made aware that Men In Black 3 has told a version of this joke before. If the joke is not new to you, please enjoy any of the single origin puns in the comments
They’re on standbi
A play on words.
My daughter, Chewbecca, not so much.
The website is now live: kengriffinlies.com. It's a must see and the site's content and layout is very professional. Let's get this trending for maximum exposure so the world will know. This isn't just a little banner on an airplane over a single city skyline --- this is massive content, data and facts that clearly show......
LIES TO CONGRESS UNDER OATH....ILLEGAL MARKET MANIPULATION....CONSPIRACY TO ARTIFICIALLY MANIPULATE AND HARM THE NORMAL MARKET PRICE DISCOVERY OF A STOCK - FOR HIS OWN PERSONAL FINANCIAL GAIN......RACKETEERING......POLITICAL CORRUPTION.....FUNNELING PAYOLA MONEY TO THE WIFE OF THE FORMER NYSE CEO - UNDER THE GUISE OF A CAMPAIGN DONATION.
When he is eventually convicted of these crimes by the federal government, Kennyboi needs to serve his time in the Bernie Madoff Memorial Prison Cell - where Bernie served the bulk of his prison sentence. Very befitting such a dastardly liar, cheat, who is a supremely parsimonious grafter!!!
Pilot on me!!
Calcium, nickel, neon
Nothing, he was gladiator.
