Phylip consensus program

In addition to serving as program committee member on various conferences, he was the program chair or co-chairs of the IEEE Intl. Conference on Data Mining. Yu received the B. Degree in E. Multi-Hot Compact Network Embedding. Yu, Zhoujun Li. Multi-grained Named Entity Recognition. Yu, Chang-Dong Wang. Private Model Compression via Knowledge Distillation. Spectral Collaborative Filtering. Yu, and Fei Wang. Yu, Yanbo Liang, Zhoujun Li. Yu, Ann B. Ragin and Alex D. Yu and Ann B.

Yu and Jian Wu. Yu, Yuanhua Lv and Yanjie Fu. Yu, Alex D. Leow and Ann B. Yu, Heide Klumpp and Alex D. Yu and Jiawei Han. Yu and Yuanhua Lv. Yu, Yuanhua Lv and Qianyi Zhan. Yu and Alex D. Yu, Linlin Shen and Ann B. Yu and Ming-Syan Chen. This lab complements some of the exercises in the Virtual Neurophysiology lab. Modeling resting potentials in Neurons Modeling action potentials Modeling the delayed rectifier Potassium channels Modeling the sodium ion channel and its effects on neural signaling Current Clamp protocol Voltage Clamp Protocol Understanding Frequency-Current relationship Understanding first spike latency - current relationship Voltage-Current VI plot Effects of pharmacological blockers on action potential Biochemistry Virtual Lab I Biochemistry is the study of the chemical processes in living organisms.

It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules. The experiments included in Biochemistry Virtual Lab I are fundamental in nature, dealing with the identification and classification of various carbohydrates, acid-base titrations of amino acids, isolation of proteins from their natural sources, etc.

Population ecology is the study of populations especially population abundance and how they change over time. Crucial to this study are the various interactions between a population and its resources. Studies on simple models of interacting species is the main focus this simulation oriented lab.

Studies based on models of predation, competition as seen in interacting species is the main focus this simulation oriented lab.

Lab II focuses on applied principles of population ecology for PG students. This includes eukaryotes such as fungi and, protists and prokaryotes. Viruses, though not strictly classed as living organisms, are also studied. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

It includes the study of the structure and organization, growth, regulation, movements and interaction of the cells. Once that is done, TextEdit also has a checkbox in the Save As window that defaults to providing a. Save As also may have a check box that defaults to hiding the three-letter extension of the file, so that when the file is saved as say foofile. It is best to uncheck that box. For these word processors, the next time you edit the same file, using Save , the program should use those settings without asking you.

If you have some trouble getting an input file that the programs can read, look into whether you properly set these options. This can be usually be done by using the Save As choice in the File menu and making the right settings. Text editors such as the vi and emacs editors on Unix and Linux and available on Mac OS X too , or the pico editor that comes with the pine mailer program, produce their files in Text Only format and should not cause any trouble.

The format of the input files is discussed below, and you should also read the other PHYLIP documentation relevant to the particular type of data that you are using, and the particular programs you want to run, as there will be more details there.

The programs interact with the user by presenting a menu. Aside from the user's choices from the menu, they read all other input from files. These files have default names. The program will try to find a file of that name - if it does not, it will ask the user to supply the name of that file.

Input data such as DNA sequences comes from a file whose default name is infile. If the user supplies a tree, this is in a file whose default name is intree.

Values of weights for the characters are in weights , and the tree plotting program need some digitized fonts which are supplied in fontfile all these are default names.

Where the files are When you run a program, you are in a current folder. If you run it by clicking on an icon, the folder is the one that has the icon. If you run it by typing the name of the program, the folder is the current folder when you do that. The program will look for default files such as infile and intree in that folder.

When it writes files, their default locations are also in the current folder. The program need not actually be in the current folder. An icon can sometimes be a link to a program located elsewhere. The operating system maintains a default path for your account, which is a series of names of folders.

When you type the name of a program, the operating system will look in that series of folders until it finds the program, and then run it. But in all of these cases, the input and output files will, by default, be in the current folder, even if the program is located in some other folder. Users can change where the input files are, or where the output files go. If no file called infile is found in the current folder, you will be asked to type the name of the file.

A similar process occurs when the program cannot find file intree. When the program starts to write an output file, such as outfile , a similar series of events happens, with one important difference. It is when a file outfile already exists in the current folder that the user will be asked what to do.

In the case of input files, it was when they did not exist that the user is asked what to do. You will be given the opportunity to Replace the file, Append to the file, write to a different File, or Quit.

Understanding which folder is the current folder, and whether there are files named infile , intree , outfile , or outtree there, is crucial to successfully running PHYLIP programs, and making sure that they analyze the correct data set and write their files in the right place.

Data file format I have tried to adhere to a rather stereotyped input and output format. These are in free format, separated by blanks. The information for each species follows, starting with a ten-character species name which can include blanks and some punctuation marks , and continuing with the characters for that species.

The name should be on the same line as the first character of the data for that species. I will use the term "species" for the tips of the trees, recognizing that in some cases these will actually be populations or individual gene sequences.

The name should be ten characters in length, and either terminated by a Tab character or filled out to the full ten characters by blanks if shorter.

If you forget to extend the names to ten characters in length by blanks, and do not terminate them with a Tab character, the program will get out of synchronization with the contents of the data file, and an error message will result. A Tab character that terminates a name will not be taken as part of the name that is read; the name will then automatically be filled with blanks to a total length of 10 characters.

In the discrete-character programs, DNA sequence programs and protein sequence programs the characters are each a single letter or digit, sometimes separated by blanks. In the continuous-characters programs they are real numbers with decimal points, separated by blanks: Latimeria 2.

The molecular sequence programs can take the data in "aligned" or "interleaved" format, in which we first have some lines giving the first part of each of the sequences, then some lines giving the next part of each, and so on.

The blank line which separates the two groups of lines the ones containing sites and ones containing sites may or may not be present. It is important that the number of sites in each group be the same for all species i. Alternatively, an option can be selected in the menu to take the data in "sequential" format, with all of the data for the first species, then all of the characters for the next species, and so on.

This is also the way that the discrete characters programs and the gene frequencies and quantitative characters programs want to read the data. They do not allow the interleaved format.

In the sequential format, the character data can run on to a new line at any time except in the middle of a species name or, in the case of continuous character and distance matrix programs where you cannot go to a new line in the middle of a real number.

Thus it is legal to have: Archaeopt or even: Archaeopt though note that the full ten characters of the species name must then be present: in the above case there must be a blank after the "t". In all cases it is possible to put internal blanks between any of the character values, so that Archaeopt is allowed. Note that you can convert molecular sequence data between the interleaved and the sequential data formats by using the Rewrite option of the J menu item in Seqboot.

If you make an error in the format of the input file, the programs can sometimes detect that they have been fed an illegal character or illegal numerical value and issue an error message such as BAD CHARACTER STATE: , often printing out the bad value, and sometimes the number of the species and character in which it occurred.

The program will then stop shortly after. One of the things which can lead to a bad value is the omission of something earlier in the file, or the insertion of something superfluous, which cause the reading of the file to get out of synchronization. The program then starts reading things it didn't expect, and concludes that they are in error.

So if you see this error message, you may also want to look for the earlier problem that may have led to the program becoming confused about what it is reading. Some options are described below, but you should also read the documentation for the groups of the programs and for the individual programs. The Menu The menu is straightforward. It typically looks like this this one is for Dnapars : DNA parsimony algorithm, version 3. Yes S Search option? More thorough search V Number of trees to save?

Use input order O Outgroup root? No, use as outgroup species 1 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 Y to accept these or type the letter for one to change If you want to accept the default settings they are shown in the above case you can simply type Y followed by pressing on the Enter key. If you want to change any of the options, you should type the letter shown to the left of its entry in the menu.

For example, to set a threshold type T. Lower-case letters will also work. For many of the options the program will ask for supplementary information, such as the value of the threshold. Note the Terminal type entry, which you will find on all menus. It allows you to specify which type of terminal your screen is. Choosing zero 0 toggles among these three options in cyclical order, changing each time the 0 option is chosen.

If one of them is right for your terminal the screen will be cleared before the menu is displayed. If none works, the none option should probably be chosen. The programs should start with a terminal option appropriate for your computer, but if they do not, you can change the terminal type manually. This is particularly important in program Retree where a tree is displayed on the screen - if the terminal type is set to the wrong value, the tree can look very strange. The other numbered options control which information the program will display on your screen or on the output files.

The option to Print indications of progress of run will show information such as the names of the species as they are successively added to the tree, and the progress of rearrangements. You will usually want to see these as reassurance that the program is running and to help you estimate how long it will take. But if you are running the program "in background" as can be done on multitasking and multiuser systems, and do not have the program running in its own window, you may want to turn this option off so that it does not disturb your use of the computer while the program is running.

Note also menu option 3, "Print out tree". This can be useful when you are running many data sets, and will be using the resulting trees from the output tree file. It may be helpful to turn off the printing out of the trees in that case, particularly if those files would be too big. The Output File Most of the programs write their output onto a file called usually outfile , and a representation of the trees found onto a file called outtree. The exact contents of the output file vary from program to program and also depend on which menu options you have selected.

For many programs, if you select all possible output information, the output will consist of 1 the name of the program and its version number, 2 some of the input information printed out, and 3 a series of phylogenies, some with associated information indicating how much change there was in each character or on each part of the tree.

The numbers at the forks are arbitrary and are used if present merely to identify the forks. For many of the programs the tree produced is unrooted. Rooted and unrooted trees are printed in nearly the same form, but the unrooted ones are accompanied by the warning message: remember: this is an unrooted tree! Mathematicians still call an unrooted tree a tree, though some systematists unfortunately use the term "network" for an unrooted tree.

This conflicts with standard mathematical usage, which reserves the name "network" for a completely different kind of graph. The root of this tree could be anywhere, say on the line leading immediately to Mouse. It is important also to realize that the lengths of the segments of the printed tree may not be significant: some may actually represent branches of zero length, in the sense that there is no evidence that those branches are nonzero in length.

Some of the diagrams of trees attempt to print branches approximately proportional to estimated branch lengths, while in others the lengths are purely conventional and are presented just to make the topology visible.

You will have to look closely at the documentation that accompanies each program to see what it presents and what is known about the lengths of the branches on the tree. The above tree attempts to represent branch lengths approximately in the diagram. But even in those cases, some of the smaller branches are likely to be artificially lengthened to make the tree topology clearer.

When a tree has branch lengths, it will be accompanied by a table showing for each branch the numbers or names of the nodes at each end of the branch, and the length of that branch. For the first tree shown above, the corresponding table is: Between And Length Approx. Confidence Limits 1 Bovine 0. Similar tables exist in distance matrix and likelihood programs, as well as in the parsimony programs Dnapars and Pars. Some of the parsimony programs in the package can print out a table of the number of steps that different characters or sites require on the tree.

This table may not be obvious at first. Thus site 23 is column "3" of row "20" and has 1 step in this case. There are many other kinds of information that can appear in the output file, They vary from program to program, and we leave their description to the documentation files for the specific programs.

The Tree File In output from most programs, a representation of the tree is also written into the tree file outtree. The tree is specified by nested pairs of parentheses, enclosing names and separated by commas. We will describe how this works below. Trailing blanks in the name may be omitted. The pattern of the parentheses indicates the pattern of the tree by having each pair of parentheses enclose all the members of a monophyletic group. The tree file could look like this: Mouse,Bovine , Gibbon, Orang, Gorilla, Chimp,Human ; In this tree the first fork separates the lineage leading to Mouse and Bovine from the lineage leading to the rest.

Within the latter group there is a fork separating Gibbon from the rest, and so on. The entire tree is enclosed in an outermost pair of parentheses. The tree ends with a semicolon.

In some programs such as Dnaml, Fitch, and Contml, the tree will be unrooted. The single three-way split corresponds to one of the interior nodes of the unrooted tree it can be any interior node of the tree.

The remaining forks are encountered as you move out from that first node. In newer programs, some are able to tolerate these other forks being multifurcations multi-way splits. You should check the documentation files for the particular programs you are using to see in which of these forms you can expect the user tree to be in.

Note that many of the programs that actually estimate an unrooted tree such as Dnapars produce trees in the treefile in rooted form! This is done for reasons of arbitrary internal bookkeeping.

The placement of the root is arbitrary. We are working toward having all programs be able to read all trees, whether rooted or unrooted, multifurcating or bifurcating, and having them do the right thing with them. But this is a long-term goal and it is not yet achieved.

For programs that infer branch lengths, these are given in the trees in the tree file as real numbers following a colon, and placed immediately after the group descended from that branch. Here is a typical tree with branch lengths: cat These representations of trees are a subset of the standard adopted on 24 June at the annual meetings of the Society for the Study of Evolution by an informal committee its final session in Newick's lobster restaurant - hence its name, the Newick standard consisting of Wayne Maddison author of MacClade , David Swofford PAUP , F.

Day, and me. This standard is a generalization of PHYLIP's format, itself based on a well-known representation of trees in terms of parenthesis patterns which is due to the famous mathematician Arthur Cayley, and which has been around for over a century. The standard is now employed by most phylogeny computer programs but unfortunately has yet to be decribed in a formal published description. Options are selected in the menu. Common options in the menu A number of the options from the menu, the U User tree , G Global , J Jumble , O Outgroup , W Weights , T Threshold , M multiple data sets , and the tree output options, are used so widely that it is best to discuss them in this document.

The U User tree option. This option toggles between the default setting, which allows the program to search for the best tree, and the User tree setting, which reads a tree or trees "user trees" from the input tree file and evaluates them. The input tree file's default name is intree. In many cases the programs will also tolerate having the trees be preceded by a line giving the number of trees: Alligator,Bear , Cow, Dog,Elephant ,Ferret ; Alligator,Bear , Cow,Dog ,Elephant ,Ferret ; Alligator,Bear , Cow,Dog , Elephant,Ferret ; An initial line with the number of trees was formerly required, but this now can be omitted.

Some programs require rooted trees, some unrooted trees, and some can handle multifurcating trees. You should read the documentation for the particular program to find out which it requires. Program Retree can be used to convert trees among these forms on saving a tree from Retree, you are asked whether you want it to be rooted or unrooted.

In using the user tree option, check the pattern of parentheses carefully. The programs do not always detect whether the tree makes sense, and if it does not there will probably be a crash hopefully, but not inevitably, with an error message indicating the nature of the problem. Trees written out by programs are typically in the proper form. The G Global option. In the programs which construct trees except for Neighbor, the " In most of these programs the rearrangements are automatically global, which in this case means that subtrees will be removed from the tree and put back on in all possible ways so as to have a better chance of finding a better tree.

Since this can be time consuming it roughly triples the time taken for a run it is left as an option in some of the programs, specifically Contml, Fitch, Dnaml and Proml. In these programs the G menu option toggles between the default of local rearrangement and global rearrangement.

The rearrangements are explained more below. The J Jumble option. In most of the tree construction programs except for the " In these programs J option enables you to tell the program to use a random number generator to choose the input order of species.

This option is toggled on and off by selecting option J in the menu. The program will then prompt you for a "seed" for the random number generator. Each different seed leads to a different sequence of addition of species.

By simply changing the random number seed and re-running the programs one can look for other, and better trees. If the seed entered is not odd, the program will not proceed, but will prompt for another seed.

The Jumble option also causes the program to ask you how many times you want to restart the process. If you answer 10, the program will try ten different orders of species in constructing the trees, and the results printed out will reflect this entire search process that is, the best trees found among all 10 runs will be printed out, not the best trees from each individual run.

Some people have asked what are good values of the random number seed. The random number seed is used to start a process of choosing "random" actually pseudorandom numbers, which behave as if they were unpredictably randomly chosen between 0 and 2 32 -1 which is 4,,, You could put in the number and find that the next random number was ,, However if you re-use a random number seed, the sequence of random numbers that result will be the same as before, resulting in exactly the same series of choices, which may not be what you want.

The O Outgroup option. This specifies which species is to have the root of the tree be on the line leading to it. For example, if the outgroup is a species "Mouse" then the root of the tree will be placed in the middle of the branch which is connected to this species, with Mouse branching off on one side of the root and the lineage leading to the rest of the tree on the other.

This option is toggled on and off by choosing O in the menu the alphabetic character O , not the digit 0. When it is on, the program will then prompt for the number of the outgroup the species being taken in the numerical order that they occur in the input file.

Responding by typing 6 and then an Enter character indicates that the sixth species in the data the 6th in the first set of data if there are multiple data sets is taken as the outgroup. Outgroup-rooting will not be attempted if the data have already established a root for the tree from some other consideration, and may not be if it is a user-defined tree, despite your invoking the option.

Thus programs such as Dollop that produce only rooted trees do not allow the Outgroup option. It is also not available in Kitsch, Dnamlk, Promlk or Clique. When it is used, the tree as printed out is still listed as being an unrooted tree, though the outgroup is connected to the bottommost node so that it is easy to visually convert the tree into rooted form. The T Threshold option. This sets a threshold forn the parsimony programs such that if the number of steps counted in a character is higher than the threshold, it will be taken to be the threshold value rather than the actual number of steps.

The default is a threshold so high that it will never be surpassed in which case the steps whill simply be counted. The T menu option toggles on and off asking the user to supply a threshold. The use of thresholds to obtain methods intermediate between parsimony and compatibility methods is described in my b paper.

When the T option is in force, the program will prompt for the numerical threshold value. This will be a positive real number greater than 1.

In programs Dollop, Dolmove, and Dolpenny the threshold should never be 0. The T option is an important and underutilized one: it is, for example, the only way in this package except for program Dnacomp to do a compatibility analysis when there are missing data.

It is a method of de-weighting characters that evolve rapidly. I wish more people were aware of its properties. The M Multiple data sets option. In menu programs there is an M menu option which allows one to toggle on the multiple data sets option. The program will ask you how many data sets it should expect.

The data sets have the same format as the first data set. Using the program Seqboot one can take any DNA, protein, restriction sites, gene frequency or binary character data set and make multiple data sets by bootstrapping. Trees can be produced for all of these using the M option.

They will be written on the tree output file if that option is left in force. Then the program Consense can be used with that tree file as its input file. The result is a majority rule consensus tree which can be used to make confidence intervals. The present version of the package allows, with the use of Seqboot and Consense and the M option, bootstrapping of many of the methods in the package. Programs Dnaml, Dnapars and Pars can also take multiple weights instead of multiple data sets.

They can then do bootstrapping by reading in one data set, together with a file of weights that show how the characters or sites are reweighted in each bootstrap sample. Thus a site that is omitted in a bootstrap sample has effectively been given weight 0, while a site that has been duplicated has effectively been given weight 2.

Seqboot has a menu selection to produce the file of weights information automatically, instead of producing a file of multiple data sets. It can be renamed and used as the input weights file. The W Weights option. This signals the program that, in addition to the data set, you want to read in a series of weights that tell how many times each character is to be counted.

If the weight for a character is zero 0 then that character is in effect to be omitted when the tree is evaluated. If it is 1 the character is to be counted once. Some programs allow weights greater than 1 as well. These have the effect that the character is counted as if it were present that many times, so that a weight of 4 means that the character is counted 4 times.

The values give weights 0 through 9, and the values A-Z give weights 10 through By use of the weights we can give overwhelming weight to some characters, and drop others from the analysis. In the molecular sequence programs only two values of the weights, 0 or 1 are allowed.

The weights are used to analyze subsets of the characters, and also can be used for resampling of the data as in bootstrap and jackknife resampling. For those programs that allow weights to be greater than 1, they can also be used to emphasize information from some characters more strongly than others. Of course, you must have some rationale for doing this.

The weights are provided as a sequence of digits. In cyber security, he has developed cyber-attack impact analyses for the U. He has been involved in developing educational software for Microsoft and establishing the Accenture Technology Academy.

He has produced over educational videos, has 10 years of experience with learning management systems and has made deployments in the Americas, Asia and Europe. Professor John R. He has authored and co-authored over articles in journals and conferences. Professor Williams teaches courses on the basics of programming, modern software development, web system architecture, cloud and blockchain.

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