Quiet Times

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                        This have been quite here becae I have been focing my energy on work and family. To simplify things, I’m going to foc nearly all of my blogging on the Panda’s Thumb for the time being.

                        I’ve had the good fortune of having some papers published recently. The first one is a methodology paper concerning a way of extracting phylogenetic information from regions of multiple sequence alignments that are full of indels and difficult to align:

                        PICS-Ord: unlimited coding of ambiguo regions by pairwise identity and cost scores ordination. (link)

                        Robert Lücking, Brendan P Hodkinson, Alexandros Stamatakis and Reed A Cartwright

                        BMC Bioinformatics 2011, 12:10 doi:10.1186/1471-2105-12-10

                        My co-author, Brendan Hodkinson, has already covered it on his blog.

                        In molecular biology, an alignment is a partial reconstruction of the evolutionary history of a group of sequences. In an alignment, all residues found in the same column are considered to be descended from a single residue in the ancestral sequence. (Of course, insertions violate this description, but I won’t get into that.) Alignments are not direct observations. They are actually inferences based on the patterns of sequences found in the dataset. Often times there are particular areas in which the alignment is difficult to resolve. Take this example:

                        A typical problem in multiple sequence alignments where a section is full of gaps and contains a complicated phylogenetic signal. Dark red: high certainty that alignment is accurate; Dark blue: low certainty that alignment is accurate..

                        It was constructed via the GUIDANCE webserver. (A great resource that everyone should e.) In this example, we have a region defined by a lot of sequence variation created by many insertions and deletions. The alignment is not well defined here, and in most applications it will jt be removed, and the data “thrown away”.

                        But is this the only solution? In our paper we develop a methodology, dubbed PICS-Ord (download), that provides an easy solution for extracting phylogenetic information from problematic regions chosen by its er. PICS-Ord works through a three-step process:

                        1. Realign the segments in pairs ing Ngila, and calculate the likelihood of the alignment from an evolutionary model. This produces a distance matrix of the segments.
                        2. Ordinate the distance matrix ing principal coordinate analysis (PCoA). This assigns each segment to a point in n-1-dimensional space.
                        3. Quantize each dimension into a set of characters

                        This might seem a bit odd at first. “Why not jt e the distance matrix directly?” That would be great if we could, but there aren’t any phylogenetic programs that we know off that allow the mixing of distance matrices and sequence data. With our method, we get discrete, ordered characters that can be ed in popular programs like, RAxML.

                        There are three example files in the PICS-Ord distribution, and I’ll illtrate its age with example1.fas. The alignment of these sequence fragments is messy:

                         100 114
                        sequence_001 ----------------------------------------------------------------------------tatactatcta---------------------------
                        sequence_002 -------------------------------------------------------------------aattgtatttatactatata---------------------------
                        sequence_003 -------------------------------------------------------------------tttaagatttattctatatt---------------------------
                        sequence_004 tttaggattaattttata--------------------------------------------------------taatactaatata---------------------------
                        sequence_005 -------------gatgg--------------------------------------------------------ttttacctatata---------------------------
                        sequence_006 ---------------------------------------------------------------------------tatcattatgca---------------------------
                        sequence_007 ---------------------------------------------------------------------------tatcattatgca---------------------------
                        sequence_008 -------------------------------------------------------------------------atatgtttaagata---------------------------
                        sequence_009 -------------------------------------------------------------------------atatgtttaagata---------------------------
                        sequence_010 -------------------------------------------------------------------------atatgtttaagata---------------------------
                        sequence_011 -------------gtac----------------------------------------------------------aattataatata---------------------------
                        sequence_012 -------------gtac----------------------------------------------------------aattataatata---------------------------
                        sequence_013 -------------gtac----------------------------------------------------------taatttaatata---------------------------
                        sequence_014 -------------ctac-----------------------------------------------------------aatataatata---------------------------
                        sequence_015 -------------ctac-----------------------------------------------------------aatataatata---------------------------
                        sequence_016 -------------ctac-----------------------------------------------------------attaaaatata---------------------------
                        sequence_017 -------------ctac-----------------------------------------------------------attaaaatata---------------------------
                        sequence_018 -------------gtat-----------------------------------------------------------aatttaatcta---------------------------
                        sequence_019 -------------gtat-----------------------------------------------------------attttaatcta---------------------------
                        sequence_020 -------------------------------------------------------------------------------ataagata---------------------------
                        sequence_021 -------------------------------------------------------------------------------ataagata---------------------------
                        sequence_022 --------------------------------------------------------------------------attataattaata---------------------------
                        sequence_023 --------------------------------------------------------------------------attataattaata---------------------------
                        sequence_024 -------------------------------------------------------------------------------ataagata---------------------------
                        sequence_025 -------------------------------------------------------------------------------ataagata---------------------------
                        sequence_026 ----------------------------------------------------------------------------aaaaaaaaata---------------------------
                        sequence_027 -----------------------------------------------------------------------------aaaaaaaata---------------------------
                        sequence_028 -------------------------------------------------------------------------------acaaaata---------------------------
                        sequence_029 -------------------------------------------------------------------------------acaagata---------------------------
                        sequence_030 --------------------------------------------------------------------------------acaaata---------------------------
                        sequence_031 -------------------------------------------------------------------------------acaaaata---------------------------
                        sequence_032 -------------gaat-----------------------------------------------------------aatattaaata---------------------------
                        sequence_033 -------------gaat-----------------------------------------------------------aatattaaata---------------------------
                        sequence_034 -------------gaaa-----------------------------------------------------------aatattaaata---------------------------
                        sequence_035 -------------gtat-----------------------------------------------------------tctttaatata---------------------------
                        sequence_036 -------------gtat-----------------------------------------------------------tatttaatcta---------------------------
                        sequence_037 -------------gtat-----------------------------------------------------------tatttaatata---------------------------
                        sequence_038 -------------gtat-----------------------------------------------------------tatttaatcta---------------------------
                        sequence_039 -----------------------------------------------------------------------------gttttatata---------------------------
                        sequence_040 -----------------------------------------------------------------------------gtttaatata---------------------------
                        sequence_041 -------------------------------------------------------------------------atcagtttaatacg------------------ctgagtgat
                        sequence_042 -------------------------------------------------------------------------accagtttaattta------------------ctgggtgat
                        sequence_043 ----------------------------------------------------------------------------------------------ctcagtttctgctgagtggt
                        sequence_044 ----------------------------------------------------------------------------agtttaatatg------------------ctgattgat
                        sequence_045 --------------------------------------------------------------------------------atatgta---------------------------
                        sequence_046 --------------------------------------------------------------------------------atatgta---------------------------
                        sequence_047 --------------------------------------------------------------------------------ataagta---------------------------
                        sequence_048 --------------------------------------------------------------------------------ataagta---------------------------
                        sequence_049 --------------------------------------------------------------------------------ataagta---------------------------
                        sequence_050 --------------------------------------------------------------------------------atatgta---------------------------
                        sequence_051 -----------------------------------------------------------------------------gttttctaat---------------------------
                        sequence_052 -----------------------------------------------------------------------------gtttactaaa---------------------------
                        sequence_053 -----------------------------------------------------------------------------gtttactaat---------------------------
                        sequence_054 -----------------------------------------------------------------------------gtttactaat---------------------------
                        sequence_055 -------------------------------------------------------------------------------gcta-aaa---------------------------
                        sequence_056 -------------------------------------------------------------------------------gcta-aaa---------------------------
                        sequence_057 -------------------------------------------------------------------------------gcta-aaa---------------------------
                        sequence_058 -----------------------------------------------------------------------------gtttactgaa---------------------------
                        sequence_059 -----------------------------------------------------------------------------gtttactgaa---------------------------
                        sequence_060 -----------------------------------------------------------------------------gtttactgaa---------------------------
                        sequence_061 -----------------------------------------------------------------------------gttagctgaa---------------------------
                        sequence_062 -----------------------------------------------------------------------------gttagctgaa---------------------------
                        sequence_063 -----------------------------------------------------------------------------gttagctgaa---------------------------
                        sequence_064 -------------------------------------------------------------------------------gttt-aaa---------------------------
                        sequence_065 -------------------------------------------------------------------------------gttt-aaa---------------------------
                        sequence_066 -------------------------------------------------------------------------------gttt-aaa---------------------------
                        sequence_067 -------------------------------------------------------------------------------gcta-aaa---------------------------
                        sequence_068 -------------------------------------------------------------------------------gcta-aaa---------------------------
                        sequence_069 -----------------------------------------------------------------------------atttacttaa---------------------------
                        sequence_070 -----------------------------------------------------------------------------atttacttaa---------------------------
                        sequence_071 -----------------------------------------------------------------------------atttacttaa---------------------------
                        sequence_072 ---------------------------------------------------------------------------------gttaaa---------------------------
                        sequence_073 ---------------------------------------------------------------------------------gttaaa---------------------------
                        sequence_074 aattttattaattactttagtaattaataaggttattttaagtaacagcaaaatattagttaaaagcgttgct-tgcaattagtaaagt--------------agca-ttatta
                        sequence_075 aattatattaattactttagtaattaaatttgttatttttagtaacagcaaaatattagttacaagcgttgct-tgtaattagtaaagt--------------agca-ttatta
                        sequence_076 ---------------------------------------------------------------------------------ttttta---------------------------
                        sequence_077 ---------------------------------------------------------------------------------ttttta---------------------------
                        sequence_078 ---------------------------------------------------------------------------------ttttta---------------------------
                        sequence_079 ---------------------------------------------------------------------------------ttttta---------------------------
                        sequence_080 -------------gaag-----------------------------------------------------------attaataacta---------------------------
                        sequence_081 -----------------------------------------------------------------------------atttatatta---------------------------
                        sequence_082 -----------------------------------------------------------------------------atttatatta---------------------------
                        sequence_083 actcctact------ttaaacatttagtagtgtcgaacctactgatagcatctggttttctattgg--------tacttataacataaccactaaatatttagagtattaatta
                        sequence_084 actcctact------ttaaacatttagtagtgtcgaacctactgatagcatctggttttctattgg--------tacttataacataaccactaaatatttagagtattaatta
                        sequence_085 -------------gaaa----------------------------------------------------------taacagtaacta---------------------------
                        sequence_086 -------------aaag-----------------------------------------------------------attagtaacta---------------------------
                        sequence_087 aattttaca------tttagtttttaatctttatgtttaaaa----acatgtatgctatttatatg--------tatatataatatagt--------------agaacttacaa
                        sequence_088 aattttact-------------------ttgggt-tttaaaa----actagtatgctatgtttatatattaatttatatatcatatagt--------------agaacttacaa
                        sequence_089 aattttact------ctt--tttttaagttttat-atttaaa----atctgtatgctatgtttatatattaatttatatataatatagt--------------agaacttacaa
                        sequence_090 aattttact------ctt--tttttaagttttat-atttaaa----atctgtatgctatgtttatatattaatttatatataatatagt--------------agaacttacaa
                        sequence_091 -------------gtac-----------------------------------------------------------ataataatata---------------------------
                        sequence_092 -------------gtaca--------------------------------------------------------taataataatata---------------------------
                        sequence_093 -------------gtaca--------------------------------------------------------taataataatata---------------------------
                        sequence_094 -------------gtac-----------------------------------------------------------ataataatata---------------------------
                        sequence_095 ---------------------------------------------------------------ttttttataccaataaataatata---------------------------
                        sequence_096 ---------------------------------------------------------------ttttttataccaataaataatata---------------------------
                        sequence_097 ---------------------------------------------------------------ctatttata-taataaataatata---------------------------
                        sequence_098 -------------ctat-----------------------------------------------------------ataaaaatata---------------------------
                        sequence_099 -------------ctat-----------------------------------------------------------ataaaaatata---------------------------
                        sequence_100 -------------ctat-----------------------------------------------------------ataaaaatata---------------------------
                        

                        But instead of throwing it away, you can process it with PICS-Ord and get a clean set of ordered characters that contain approximately the same phylogenetic information as the sequences above.

                            100    20
                        sequence_001 53221002101000000010
                        sequence_002 44121113101010000000
                        sequence_003 53211103102011000100
                        sequence_004 53321103111000010100
                        sequence_005 53211003101000001000
                        sequence_006 53221002001000000000
                        sequence_007 53221002001000000000
                        sequence_008 43220112011000000000
                        sequence_009 43220112011000000000
                        sequence_010 43220112011000000000
                        sequence_011 53221012011000000000
                        sequence_012 53221012011000000000
                        sequence_013 53221012011000100000
                        sequence_014 53321012001010100000
                        sequence_015 53321012001010100000
                        sequence_016 53221013001000000000
                        sequence_017 53221013001000000000
                        sequence_018 53221012001000100000
                        sequence_019 53221012001000001000
                        sequence_020 53220102011000000000
                        sequence_021 53220102011000000000
                        sequence_022 53121012011010000000
                        sequence_023 53121012011010000000
                        sequence_024 53220102011000000000
                        sequence_025 53220102011000000000
                        sequence_026 53220002001000000000
                        sequence_027 53220002001000000000
                        sequence_028 53120102011000000000
                        sequence_029 53220102011000000000
                        sequence_030 53120002011000000000
                        sequence_031 53120102011000000000
                        sequence_032 53220002111100000000
                        sequence_033 53220002111100000000
                        sequence_034 53220002111000000000
                        sequence_035 53221012011000001000
                        sequence_036 53221012001000000000
                        sequence_037 53221012011000000000
                        sequence_038 53221012001000000000
                        sequence_039 53221102111000000000
                        sequence_040 53211002011000000000
                        sequence_041 53300112011000000000
                        sequence_042 53200112011010001010
                        sequence_043 53300103001100001001
                        sequence_044 53200112001110000000
                        sequence_045 53120112001000000000
                        sequence_046 53120112001000000000
                        sequence_047 53120102001000000000
                        sequence_048 53120102001000000000
                        sequence_049 53120102001000000000
                        sequence_050 53120112001000000000
                        sequence_051 53211002011000000000
                        sequence_052 53111002011000000000
                        sequence_053 53211002011000000000
                        sequence_054 53211002011000000000
                        sequence_055 53110002001010000000
                        sequence_056 53110002001010000000
                        sequence_057 53110002001010000000
                        sequence_058 43111002011000000000
                        sequence_059 43111002011000000000
                        sequence_060 43111002011000000000
                        sequence_061 53201002011000000000
                        sequence_062 53201002011000000000
                        sequence_063 53201002011000000000
                        sequence_064 43111002011000000000
                        sequence_065 43111002011000000000
                        sequence_066 43111002011000000000
                        sequence_067 53110002001010000000
                        sequence_068 53110002001010000000
                        sequence_069 43111002011000000000
                        sequence_070 43111002011000000000
                        sequence_071 43111002011000000000
                        sequence_072 53111002001000000000
                        sequence_073 53111002001000000000
                        sequence_074 59021102011001100000
                        sequence_075 59020012001110001000
                        sequence_076 53121102001100000000
                        sequence_077 53121102001100000000
                        sequence_078 53121102001100000000
                        sequence_079 53121102001100000000
                        sequence_080 53220002001100000000
                        sequence_081 53121102001000000000
                        sequence_082 53121102001000000000
                        sequence_083 90021002001000000000
                        sequence_084 90021002001000000000
                        sequence_085 53220002000100000000
                        sequence_086 53120002000101000000
                        sequence_087 02121100001000000000
                        sequence_088 02020003000010100000
                        sequence_089 02021013011100000000
                        sequence_090 02021013011100000000
                        sequence_091 53321002001000000000
                        sequence_092 53321002011000000000
                        sequence_093 53321002011000000000
                        sequence_094 53321002001000000000
                        sequence_095 53321202010100001000
                        sequence_096 53321202010100001000
                        sequence_097 43321102011000001000
                        sequence_098 53321003001000000000
                        sequence_099 53321003001000000000
                        sequence_100 53321003001000000000
                        

                        I haven’t been keeping up with my Calix Cari polls this year for collage football. But now that the regular season has ended, I have found time to produce one. The events of this season have been rather unpredictable. Of course by the end of the season there were few surprises. Auburn appeared out of nowhere to become #1 on the strength of a once-in-a-decade player who fit perfectly into their offensive system. (Yay, for the booster who had cash to spare in this economy. We will see if their season stands the test of time.) But in my calculation Auburn is only #3, behind Oregon and ¡Stanford! (I still think Harbaugh would make a smooth transition into the coach’s chair at UGA but wouldn’t be there long. It’s good that Richt was retained.)

                        It appears my algorithm likes the Pac-10 over the SEC, and Auburn lost ground becae of its tight victories, early in the season.

                        RankTeamRecordQuality
                        1Oregon12-07.3937
                        2Stanford11-17.2491
                        3Auburn13-07.1707
                        4Oklahoma11-27.0580
                        5TCU12-06.9927
                        6Boise St11-16.8977
                        7Missouri10-26.7980
                        8Ohio State11-16.5913
                        9Texas A&M9-36.5043
                        10Oklahoma St10-26.4876

                        Ngila 1.3 Released

                        It has been a long time coming, but I have finally released Ngila 1.3. This version fixes a few bugs and includes many new features.

                        • e CMake for compilation and installation
                        • New scaling option enabled by default (identical sequences default to cost of 0)
                        • Protein evolutionary models: aazeta and aageo
                        • Fasta and Phylip format output support
                        • Cltal and Phylip format input support
                        • Report sequence identity measure
                        • Matrix output formats for distance measures
                        • Look for “ngilarc” file in the home directory.
                        • New separator option
                        • New const-align option
                        • Replace arg-file option with ngilarc option.
                        • e ctom zeta function if GSL not found.
                        • Optimize size of travel table.
                        • Ordering of –pairs-all fixed
                        • bug fix for output of large alignments >10kb
                        • minor bug fix for geo model

                        The Working Life

                        | 1 Comment

                        I apologize for things being slow on this blog. I’ve been knee deep in programming, mancripts, grant proposals, and teaching. I’m hoping to have results to share in the near future. In the mean time, you can follow some of my activities on the Panda’s Thumb.

                        I will say that the development version of Dawg now supports codon models, and Ngila has some new features as well.

                        Odd Hack

                        | 1 Comment

                        This machine got partially hacked over the weekend. From what I can tell, Ziproxy was compromised and ed to submit spam email through my system. Becae my mail sever accepts local email, it was going out. It looks like only yahoo emails were being hit. Of course, the spam was coming from China.

                        Since I turned off Ziproxy, I haven’t seen any odd email originating from my machine.

                        Dawg 2

                        | 3 Comments

                        Dawg created its first protein sequences today. Woot!

                        Bama Wins 2009 Calix Cari

                        | 1 Comment

                        The announcement is a bit late, but after beating Texas, Bama has won the 2009 Calix Cari.

                        RankTeamRecordQuality
                        1Alabama14-07.8239
                        2Florida13-17.4268
                        3Texas13-17.1820
                        4TCU12-16.8893
                        5Oregon10-36.7193
                        6Virginia Tech10-36.7187
                        7Ohio State11-26.7114
                        8Boise St14-06.6326
                        9Cincinnati12-16.5913
                        10Iowa11-26.4511
                        11Georgia Tech11-36.4444
                        12Penn State11-26.3350
                        13Brigham Young11-26.1872
                        14LSU9-46.1531
                        15Pittsburgh10-36.0738
                        16Southern Cal9-46.0535
                        17Miami FL9-46.0213
                        18Nebraska10-46.0208
                        19Oklahoma8-55.8503
                        20Wisconsin10-35.8343
                        21Arkansas8-55.7899
                        22Utah10-35.7644
                        23Clemson9-55.7595
                        24Mississippi9-45.7330
                        25Arizona8-55.6809
                        26Stanford8-55.6637
                        27West Virginia9-45.6543
                        28Georgia8-55.6270
                        29Texas Tech9-45.6112
                        30Oregon St8-55.6002

                        See below for the complete results of 2009.

                        Network Issues

                        We’ve been having network issues for the last week. (The network setup in general is not reliable.) Nothing is wrong with what I have control over, but I’m kind of stuck with the connection that I’ve been given.

                        My apologies to everyone this affects.

                        Calix Cari 2009 Week 14

                        With the conference championship games complete my Calix Cari rankings once again agree with the pollsters: its Texas vers Alabama for the title.

                        Surprisingly, despite Tebow crying after visiting the wood-shed in Atlanta Florida still ranks #3, ahead of undefeated teams TCU, Cincinnati, and Boise State. Two loss Oregon comes in at #4, based on its strong showings against Cal, C, Arizona, and Oregon State. Boise State produced the second best victory of the year (against Oregon) but couldn’t overcome a week conference schedule to rise higher than #9.

                        The Pac-10 placed 6 teams in the top 25, followed by Big 12 at 4, SEC, Big East, ACC, and Big 10 at 3, MWC at 2, and WAC at 1. Clearly the Pac-10’s 8-4 logjam was seen more highly than the SEC’s 7-5 logjam.

                        RankTeamRecordQuality
                        1Alabama13-07.6798
                        2Texas13-07.3390
                        3Florida12-17.2858
                        4Oregon10-27.0857
                        5TCU12-06.9550
                        6Cincinnati12-06.7700
                        7Virginia Tech9-36.6491
                        8Georgia Tech11-26.6343
                        9Boise St13-06.5395
                        10Ohio State10-26.4794
                        11LSU9-36.2673
                        12Iowa10-26.2457
                        13Miami FL9-36.2368
                        14Penn State10-26.1839
                        15Southern Cal8-46.1387
                        16Arizona8-46.1116
                        17Stanford8-46.0294
                        18Oregon St8-45.9837
                        19Pittsburgh9-35.9276
                        20Brigham Young10-25.8856
                        21West Virginia9-35.8317
                        22Oklahoma St9-35.8001
                        23Nebraska9-45.7685
                        24California8-45.7510
                        25Oklahoma7-55.7005

                        Snow

                        It’s snowing right now in Hoton. I’m not sure if it will stick.

                        Calix Cari 2009 Week 11

                        It’s be a few weeks since I’ve calculated my rankings for collage football, but with Uga VII passing away, I figure I’d post something in honor of him.

                        RankTeamRecordQuality
                        1Alabama10-07.5935
                        2Florida10-07.4398
                        3Texas10-07.3265
                        4TCU10-07.2566
                        5Oregon8-26.9875
                        6Georgia Tech10-16.9202
                        7Cincinnati10-06.7603
                        8Ohio State9-26.6532
                        9Virginia Tech7-36.6306
                        10Boise St10-06.6197

                        RIP Uga VII

                        Today sucks. Uga VII has died.

                        Calix Cari 2009 Week 8

                        This is my first poll of the season, and Alabama is ranked #1, followed by Iowa and Florida. What’s interesting is that a quick look through the results reveals that Boise State’s victory of Oregon is considered the best win of any team of the year.

                        RankTeamRecordQuality
                        1Alabama8-07.8141
                        2Iowa8-07.7549
                        3Florida7-07.6983
                        4Oregon6-17.5908
                        5Southern Cal6-17.5221
                        6Texas7-07.4951
                        7TCU7-07.3465
                        8Virginia Tech5-27.2887
                        9Georgia Tech7-17.1787
                        10Boise St7-07.0502

                        Happy Happy Joy Joy

                        I need to head home early today to clean up my otaku pad.

                        I have a girl coming over for a sleep over.

                        I Have a Minon

                        | 4 Comments

                        We’ve hired a master’s student to be my minion in the lab. Bwahaha…

                        Downtime

                        We’re having network issues which explains why this machine has been off the net since yesterday. It’s working now. Hopefully it will stay that way.

                        Alive in Hoton

                        Well I’ve moved to Hoton and my server is back online.

                        Moving

                        I’m moving to Hoton this weekend. Expect this website and other I administer to have limited functionality for about a week.

                        When things jt work.

                        | 7 Comments

                        I’m moving to Hoton next month, and I’m working furioly to finish up about 4 papers before I leave. Yesterday was a good day becae two things worked absolutely perfectly.

                        I’m calculating the likelihoods of some of our observations and I wrote a specific routine to do it for a first-order model. I then wrote a generic routine to calculated likelihoods for higher-order models. When I ed the generic routine to calculate the likelihood for a first-order model, I got the same result as my specialized routine. Yatah!

                        From previo analysis ing partial autocorrelations, we determined that a third-order model should explain our data the best. When I compared our models to see which one was most parsimonio (ing AIC), the third-order model again came out on top. Yatah2!

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