This document discusses building a SyMAP v5 database. It always applies to the latest release.
Referenced external docs Input Parameters and Interface MUMmer with SyMAP Demo Trouble-shoot 1. Introduction Overview and Publications Steps for finding synteny 2. Requirements System Requirements Tested platforms and timing results Perl, Java and MySQL 3. Install SyMAP Tarball External executables MySQL parameters for SyMAP	4. Demo Running the demo Two genome synteny Draft ordering Self synteny 5. New project Create a new project Input and directory structure Load project Alignment&Synteny (A&S) Draft ordering Self synteny Cancel 6. General How to update SyMAP with a new release How SyMAP Works FPC project References
Transcriptome Analysis and Comparative Transcriptomes, see TCW.

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1. Introduction

Overview

Publications

Steps for finding synteny

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Overview

SyMAP is a system for computing, displaying, and analyzing syntenic alignments between divergent eukaryotic genomes. It is designed for the comparison of a few genomes at a time (i.e. 2-4) where synteny is computed between each pair. Its features include the following:

Compute Find synteny between two sequenced eukaryotic genomes with optional annotation. Draft sequence ordering by synteny, i.e. align a draft genome to a fully sequence (not draft-to-draft). Self synteny. Query and view For multiple selected synteny pairs, display using dot plot, circular, and side-by-side. Complete queries on annotation, collinear genes, multi-hit genes, etc.

Click an image to see the closeup.

Publications

SyMAP is freely distributed software, however if you use SyMAP results in published research, you must cite one or both of the following articles along with the external program MUMmer^1,2.

        C. Soderlund, M. Bomhoff, and W. Nelson (2011)
        SyMAP: A turnkey synteny system with application to plant genomes.
        Nucleic Acids Research 39(10):e68.

        C. Soderlund,  W. Nelson, A. Shoemaker and A. Paterson (2006)
        SyMAP: A System for Discovering and Viewing Syntenic Regions of FPC maps
        Genome Research 16:1159-1168.

The back-end processing of SyMAP runs MUMmer^1,2 for the alignments (included in the tarball) and computes the synteny block from the alignment results. The SyMAP synteny algorithm is described in the above two publications, though there are many unpublished updates since publication.

Steps for finding synteny

The following three scripts are provided in the tar file.

	./xToSymap	Format files from NCBI and Ensembl into a SyMAP friendly format.
	./symap	Build the SyMAP synteny database; view and query
	./viewSymap	View and query the database results

Follow the steps below to get started with SyMAP.

1.	Use Linux or MacOS.	See system requirements.
2.	Requirements.	Set up Perl, Java and MySQL .
3.	Install SyMAP.	It is a simple unzip; see Installation and SyMAP MySQL parameters.
4.	Run the demo.	Highly recommended. See running the demo.
5.	Prepare input files.	FASTA sequence and optional GFF annotation. See Input and Creating a new project.
6.	Load the files into SyMAP.	Select Load project by the project name. See Loading project.
7.	Compute alignments and synteny.	Select Selected project beside Alignment&Synteny. See Alignment&Synteny.
8.	View results.	See User Guide for a detailed description of viewing and querying the results.

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2. Requirements

System Requirements

Tested platforms

Datasets and Timings

Disk space

Perl, Java, MySQL

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System Requirements

The machine must be a Linux or MacOS 64-bit machine with sufficient memory for your dataset.

The largest component of SyMAP execution time is running MUMmer^1,2. The time and memory for MUMmer all depends on the genomes sizes, complexity and similarity. If MUMmer fails, it is often due to insufficient memory; see the MUMmer document, which explains how to determine the problem and ways around it. It explains how to run MUMmer on a different machine and port the results to the symap_5/data/seq_results directory. The results in Tested datasets and timings gives an idea of compute times and memory.

If SyMAP runs out of memory, see Trouble Shoot.

For viewing alignments with viewSymap, CPU and memory needs are typically negligible, unless you are performing queries on more than 4-5 genomes at once.

Tested platform

SyMAP has been tested on the following:

Machine	MySQL	Java	Core (CPU)	Memory	Purchased
v5.6.6 and later:
1. MacOS M4	MySQL v8.0.42	24 from Oracle	M4 12-Core	48Gb	2025
v5.4.1 and later:
2. MacOS x86_642	MySQL v8.0.33, MariaDB 11.0.2	8, 15, 17, 18, 20 from Adoptium and Oracle	3.2 GHz 6-Core	64Gb	2018
3. Linode (Ubuntu 22.04.2 LTS)3	MySQL 8.0.33	17	Nanode	1Gb	2023
v5.4.0 and earlier:
4. Linux amd64 (Centos)4	MariaDB v10.4.12	1.8	2.3 GHz 24-Core	128Gb	2011

Tested datasets and timings

1. MacOS M4 with 48Gb has been tested with the following:
   1. The complete Homo sapiens (24 chrs, 3Gb) with Mus musculus (21 chrs, 2.7Gb).
      To get MUMmer to run successfully, it was necessary to uncheck Concat.

   2. Chr 5,17,X,Y of Homo sapiens (478Mb) and Pan troglodytes (447Mb);
      Chr 11,13,X,Y of Mus musculus (504Mb); Chr 11,19,X of Oryctolagus cuniculus (257Mb).

   3. Arabidopsis thaliana (5 chr, 119Mb), Brassica rapa (10 chr, 297Mb), Brassica oleracea (9 chr, 447Mb).

   4. Peach Prunus persica (8 chr, 227Mb) and draft Prunus yedoensis (250 scaffolds, 408Mb).
      Pyeudo.Peach was the result of ordering Pyedo against peach (8 chr, 270Mb).

   Times are those reported in the SyMAP output, which uses the Java system time functions (clock times are greater than the Java CPU system times). Repeated execution can result in times varying by approximately +/-5secs. All the following results use 4 CPUs (thread/core).

   Species	MUMmer	SyMAP		Size
   Hsa x Mus	30h:45m	1m:37s		3Gb x 2.7Gb, large genomes
   Hsa x Pan	16h:40m	0m:35s		478Mb x 447Mb, closely related
   Hsa x Mus	0h:55m	0m:04s		478Mb x 504Mb
   A.thal x B.oler	0h:31m	1m:14s		119Mb x 447Mb
   B.raba x B.oler	4h:23m	4m:12s		297Mb x 447Mb, closely related
   Peach x Pyedo	0h:44m	6m:51s		227Mb x 408Mb, Pyedo ordered by peach
   Peach x Pyedo.Peach	0h:40m	0m:20s		227Mb x 270Mb

2. MacOS x86_64 with 64Gb has been tested on 2-4 above. For comparison, the following A&S was computed with 4 CPUs; note the longer time for the synteny computation on the older Mac machine.

   Species	MUMmer	SyMAP
   A.thal x B.oler	0h:33m	4m:06s

3. Linode nanode with 1Gb was too small to run MUMmer, so the MUMmer demo result files were transfered to the data/seq_results/demo_seq_to_demo_seq2 directory. This allowed all other features to be tested on the demo, including running the synteny algorithm without the alignment. Also, two tiny input files were used to test MUMmer.

4. Linux amd64 with 128Gb was used extensively on large plant genomes.
   To align rice x maize (400Mb x 2365Mb) required a total of 1h:3m using 8 CPUs

Disk space

Given the amazing disk space available for all modern computers, disk space should not be a problem. MUMmer produces a .mum and .delta file; SyMAP only uses the .mum file so it removes the MUMmer alignment .delta file. For the full Homo sapiens x Mus musculus, the resulting data/seq_results/Hsa_to_Mus/align directory was 573M.

You can remove the data/seq_results/<project1_to_project2>/ directory after SyMAP has finished the synteny computation, but it is strongly recommended that you leave them if you have the space. There are frequent SyMAP updates with improvements to the clustering and synteny computations; if you have kept these files, then you can update your database in very little time (note the >30h for MUMmer for Hsa x Mus versus 1m:37s for the synteny). Also, you can easily try different parameters for the clustering and synteny stages.

If you do not want SyMAP to remove the .delta, use the "-mum" command line argument.

Perl, Java and MySQL

Perl: This is for MUMmer; see MUMmer manual, section on Software Requirements. It states that the following are required: Perl5 (5.6.0), sh, sed, awk (the last 3 are standard on any linux-based machine).

Java: You must have Java version 17.0.11 or later. The released symap.jar file has been compiled with Java 17.0.11, which is upward compatible.

MySQL: If your machine does not have MySQL or MariaDB, download and install it. For example, MySQL can be downloaded from dev.mysql.com. On a personal MacOS, simply download the '.dmg' file and following the instructions. On a work server, the system administrator may need to install it.

Important Note: The default settings of MySQL are poorly suited for large-scale data storage. You will want to adjust the parameters innodb_buffer_pool_size and innodb_flush_log_at_trx_commit as described in Trouble Shoot MySQL.

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3. Install SyMAP

Tarball

Externals executables

MySQL parameters

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Tarball

Installation consists of unzipping the download tarball using the command

     > tar -xf symap_5.tar.gz

This can be done anywhere and it creates a directory called symap_5. You can move this directory later if desired. The contents are:

   LICENSE   README   data/   ext/   java/
   scripts/  symap.config     symap  viewSymap  xToSymap

Data: The data/ directory contains a seq/ sub-directory, which contains the demo files, and is the default location for all input sequence files. The symap script expects to find the data directory, the viewSymap does not.

External executables

The ext/ directory contains the external programs MUMmer^1,2 for sequence alignment, and MAFFT⁶ and MUSCLE⁷ for interactive MSA alignment (for Queries). The directory contains:

	README		mummer/		mummer4/	muscle/		mafft/

Each has subdirectories:

Subdirectory	OS (Architecture)	Note
lintel64	Linux
mac	Mac OS X (x86_64)
macM4	Mac OS X (M4 silicon)	No muscle executable

SyMAP will determine which subdirectory to use.

If you compile your own executables for a different machine (architecture), do the following:

1. Under mummer and mafft, make a directory with your machine name.
2. Put the executables under this directory in the exact same way as shown for lintel64.
3. In the symap configuration file (default symap.config), add a line

        arch={your directory architecture name}

Note that I do not have an alternative machine to try this on, but it should work. Email me at symap@agcol.arizona.edu if it does not.

For MUMmer, see Executables and Using MUMmer4. On MacOS, you may also need to view MacOS externals.

MySQL parameters for SyMAP

Parameters for accessing the MySQL database should be set in the symap.config file in the main symap directory, as follows:

Database Parameters
db_name	Name of the MySQL database, which SyMAP will create when it first reads >symap.config. It is standard to start the name with symap, e.g symapDemo.
db_server	The machine hosting the MySQL database, e.g. myserver.myschool.edu. If using your local machine, enter localhost.
db_adminuser	MySQL username of a user with sufficient privileges to create a database. It is also necessary for loading, deleting and running synteny.
db_adminpasswd	Password of the admin user.
db_clientuser	Optional: MySQL username of a user with read-only access. This is only necessary if you want a machine to run viewSymap as read-only.
db_clientpasswd	Optional: Password of the client user (if db_clientuser is non-blank).

Example symap.config.

  db_name             = symapDemo
  db_server           = localhost
  db_adminuser        = <adminid>
  db_adminpasswd      = <password>
  db_clientuser       =
  db_clientpasswd     =

To use an alternative file than symap.config, use the "-c" command line argument, e.g.

  >./symap -c symapTmp.config

This is useful if you have multiple SyMAP databases.

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4. Demo

Running the demo

Two genome synteny

Draft ordering

Self synteny

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Running the Demo

If you have not used SyMAP before, it is essential to run the demos. After you have installed MySQL, do the following:

1. Change into the symap_5 directory.

2. Edit symap.config and enter database and host information (see MySQL).

3. From the command line, type ./symap.

The first time you run SyMAP, it will create the database with information written to the terminal, e.g.

Creating database 'symapDemo' (jdbc:mysql://localhost/symapDemo?characterEncoding=utf8).

It will check your MySQL variables; if there are any "Suggested" changes, see Trouble Shoot MySQL.

It will also check that the provided external programs (e.g. MUMmer) are executable; if it shows any problems, see Executables. For MacOS, you may also need MacOS externals.

Demo two genome synteny

Executing ./symap will bring up the Manager panel as shown on the lower right; it will show the three demo projects provided with the SyMAP tarball.
Check Demo-Seq and Demo-Seq2 and they will be displayed on the right panel. A link Load All Projects will be displayed at the top of the right panel; select it to load the projects, which will take several minutes. If loading the Demo-Seq takes more than a few minutes, you may need to adjust the MySQL parameters, see TroubleShoot MySQL.	Project Manager
When done, the Manager will look like the image shown on the right. Your may verify the results by selecting the View link. In the Available Syntenies table, the cell for Demo_Seq2 and Demo_Seq will automatically be selected (green cell). Click the Selected Pair button to start the Alignment&Synteny. All Pairs button can also be selected, as it will perform Alignment&Synteny on all pairs in the table.
The Alignment&Synteny takes less than 5 minutes on the MacOS 10.5 but could take up to 30 minutes on a slow machine. When done, the table will have a checkmark (✓), signifying that the synteny is available for viewing.
Click Summary to view the summary shown on the right; there may be slight differences in the #Cluster hits because of different numbers of CPUs, MacOS vs Linux, etc (but the #Blocks come out the same). To view the other interfaces, see Demo Results.   Once the alignments are computed, the A&S parameters can be experimented without having to redo the alignments. Try using the Algorithm 2 (exon-intron) for Cluster Hits by clicking the Parameters button, which opens the Parameters panel, then select Algorithm 2 and Save. Click Selected Pairs (Redo) which will result in a summary similar to this.

Demo draft ordering

Load the Demo-Draft project. Select Demo-Seq2 on the left side so it shows in the Available Syntenies. Select the Demo-Draft/Demo-Seq2 cell. Open the Parameters panel; at the bottom, select Draf->Seq2.
Run the Alignment&Synteny, where the alignment should take less than 10 minutes with one CPU. When done, open the Summary for the pair which will be similar to what is shown on the right; as mentioned above, there may be slight difference in the number of Cluster hits. See the first dot plot in Demo-draft. It is recommended that the Cluster Algo1 be used for ordering sequence.

The ordering algorithm creates the following files and directories:

1. File of ordered contigs: It writes the order of the contigs along with whether they should be flipped to a file called /data/seq/demo_draft/demo_seq2_ordered.csv.

2. New project: It creates a new project directory called data/seq/draft_demo..demo_seq2 (the naming allows demo_draft to unambiguously be ordered against different genomes). This directory will contain a sub-directory /sequence which contains the sequence file.

3. FASTA sequence file of ordered sequences: The sequence file will contain the ordered contigs that are flipped when appropriate. The chromosome names correspond to the order-against project (e.g. demo_seq2). Chromosome 'chr0' contains all draft sequences that were not placed.

The new project is shown on the left side of the Manager. The display name is Demo_Draft.Demo_seq2, click and load it.

Running the Alignment&Synteny between the Demo_Draft.Demo_seq2 project and Demo_seq2 will provide a more coherent display (see the second dot plot for Demo-Draft). Using the project's Parameters panel, the Demo_Draft.Demo_Seq2 display name can be shortened.

Demo self synteny

To perform self synteny, select the cell for Demo_seq row and column (it turns green) followed by Selected Pair. This computes very few blocks, as shown in Demo self synteny.

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5. New project

Create

Input and directory

Load project

Alignment & Synteny

Draft ordering

Self synteny

Cancel

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Create a new project

Database name: The parameter db_name (database name) in the symap.config file that comes with the tar file is set to symapDemo. Edit the symap.config file to set the database name to something more meaningful. It is protocol to start the database name with 'symap'.

The following gives an outline of the steps and important details of the directory structure, linking to the appropriate sections in Interface and parameters document, which details all functions and parameters.

Input and directory structure

Input: See Input for description of the sequence (FASTA) and annotation (GFF) files. The xToSymap interface takes as input NCBI or Ensembl files, and outputs the best input files for SyMAP, along with automatically creating the correct directory structure.

Project-name: Each project has a project-name, which is also the project's directory name. The project-name should be a short descriptive name; see the Input's Project directory for important details. The use of the project-name is shown below.

Project directory structure:

Each project has a directory as follows:

  /data/seq/<project-name>

The default location for sequence and annotation files is:

  /data/seq/<project-name>/sequence
  /data/seq/<project-name>/annotation

To indicate to the symap Load project function where the project's input files are, do one of the following three:

1. Create these sub-directories under /data/seq and put your files there,
   e.g using project-name=foobar:

     cd data/seq
     mkdir foobar
     cd foobar
     mkdir sequence
     mkdir annotation
   

   Move your FASTA file(s) to data/seq/<project-name>/sequence (e.g. data/seq/foobar/sequence) and your optional GFF files(s) to data/seq/<project-name>/annotation (e.g. data/seq/foobar/annotation)

2. Create these sub-directories under /data/seq and use soft links to point to the file locations,
   e.g using project-name=foobar:

     cd data/seq
     mkdir foobar
     cd foobar
     ln -s <location of directory of sequence files> sequence
     ln -s <location of directory of annotation files> annotation
   

3. Use the Add project button on the symap interface (lower-left corner) to add the project name to the data/seq directory. Use the project's parameter panel to enter the location of the sequences and optional annotation files into the Sequence files and Anno files parameters.

For options 1 and 2, it is not necessary to enter the locations of the files in the project parameter panel since both use the default locations.

All sub-directories in data/seq are shown on the left-panel of the symap interface.

Each project is shown with its Display name, which is set in the project's parameters. The project-name is shown on the right hand image as the Directory name, as they are the same.

The symap program requires the directories to be present (and will create them if necessary), viewSymap does not.

Load project

See project parameters on setting the parameters. See Load for loading a project.

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Alignment&Synteny

See Parameters on setting the pair parameters for the this step. See CPU and Verbose for a description of these two options. Then select Selected Pair to run the Alignment&Synteny.

Alignment&Synteny files: The result files are in the following directories:

   /data/seq_results/<project-name1>-to-<project-name2>/align
   /data/seq_results/<project-name1>-to-<project-name2>/final

As mentioned in Disk, after the database is complete, these can be removed. However, sometimes SyMAP version updates require the project files to be reloaded and/or the synteny to be recomputed; if these files remain, the existing MUMmer files will be used, which saves a lot of time.

The log files are in the /logs directory, see Running MUMmer for more details.

See Using MUMmer with SyMAP for a discussion on how it works in SyMAP, trouble-shooting, and running MUMmer externally (i.e. if your local machine does not have enough memory or CPUs, you may need to run it on a bigger machine).

Incomplete alignment If SyMAP completed the alignment, e.g. the demo /align directory will have the following files:

-rw-r--r--@ 1 cari  staff     0B Apr 10 10:28 all.done
-rw-r--r--@ 1 cari  staff   1.2M Apr 10 10:28 demo_seq_cc.demo_seq2_f1.mum
-rw-r--r--@ 1 cari  staff     0B Apr 10 10:28 demo_seq_cc.demo_seq2_f1.mum.done
-rw-r--r--@ 1 cari  staff   541K Apr 10 10:27 demo_seq_cc.demo_seq2_f2.mum
-rw-r--r--@ 1 cari  staff     0B Apr 10 10:27 demo_seq_cc.demo_seq2_f2.mum.done

1. The 'all.done' indicates that the all alignments completed.
2. If 'all.done' does not exist, SyMAP will perform any alignments that do NOT have a corresponding 'mum.done'. If the Concat setting has been switched between the previous and current run, this will not work correctly.
3. If the user supplied the alignments (Supply MUMmer files), there may not be 'mum.done' files but there should be an 'all.done', so it is assumed they are all done.

Draft alignment and ordering

If you are ordering the draft sequence against a closely related sequenced genome, see demo draft on how to proceed. It is strongly suggested you run the demo! In a nutshell, the steps are:

1. Load both sequences.
2. Open the pairs's Parameters panel. At the bottom of the panel, select the radio button that indicates ordering your draft against a complete sequence (e.g. Draf->Seq2).
3. Run the Alignment&Synteny (A&S). At the end, you will see a new project with the two project-names separated by ".." in the left panel. It will contain:
   • A sequence directory with a ".fa" FASTA file. Any scaffolds matching the Order against genome will be assigned the same chromosome name. All scaffolds aligning to an Order against chromosome will be appended together in order with 100 N's between each scaffold. Any extra sequences will be put in ">Chr0".
   • An annotation directory with a ".gff" file that specifies where the gaps are.
4. Load the new project. Then run A&S between this new project and the original whole genome project.

The original draft directory will have a new file with the suffix ordered.csv that will contain the merged contigs and what chromosome number they are mapped to.

If the draft sequence is in too many sequence contigs, it takes a long time for the MUMmer comparisons. Also, the displays are very cluttered to the point of unreadable, but these will generally be merged in step 4 above, so the new display is fine. Nevertheless, you may want to remove the smallest contigs. This can be done by limiting the number of sequence contigs by setting Minimum length in the project's Parameter panel to only load the largest 150 sequences. To determine the minimal length, use the Lengths button in the xToSymap interface, which will print out all the lengths; set the Minimum length to the 150th length.

Self synteny

To perform self synteny, select the cell for the same project (it turns green) followed by Selected Pair (the All Pairs option does not include self synteny).

By default, SyMAP uses the MUMmer 'NUCmer' program for self-alignments. Each chromosomes is compared to every other chromosome including itself.

The Alignment&Synteny Parameters panel has an option to set Self Args, which is only used when comparing the chromosome sequence file to itself. Make sure that the Cluster Hits Algorithm 1 option is selected.

A better demonstration than the demo is to download Arabidopsis thaliana from NCBI, convert it with the NCBI convert script, and run the self synteny. It took 16 minutes with one processor on a Mac Mini (2018) with 64Gb main memory. The dot plot is shown on the right (click on the image for a closeup view).

Cancel

The Load and A&S methods have a popup progress panel, as shown on the right. There is a Cancel button on the bottom that can be clicked to cancel the execution; it will remove the results from the database and exit. Occasionally, the Cancel will cause it to create an error, writing to the error.log or to the terminal. This is not a problem, though you may need to remove the results yourself. If MUMmer is running when you Cancel, make sure there is "Error: Failed command:" line to terminal for each MUMmer alignment that was running; if there is not, use the "top" linux command to view the running processes and stop any MUMmers still running.

Also, see Trouble Shoot Hang

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6. General

Update

How SyMAP works

FPC

References

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How to update SyMAP with a new release

If you have been working with SyMAP and have existing projects:

• If the symap.jar is available from the download site and there are only changes to it, download it and replace the one in symap_5/java/jar.

or if there are changes to more than the jar file:

• Put the new symap_5.tar.gz in a permanent location and untar it.
• Replace the /data and symap.config from your previous SyMAP location to this new location.
• This approach is safest as it acquires all changes (e.g. scripts) except for changes to the demo files.

or

• Put the new symap_5.tar.gz in a temporary location and untar it.
• Move symap_5/java/jar/symap.jar to the java/jar location of your permanent SyMAP.
• Check to see if there are any /scripts or /ext changes that need to also be copied over.

The Alignment&Synteny will use existing MUMmer files if they have not been removed.

How SyMAP Works

This section provides a brief overview of the SyMAP processing steps; for more, see the SyMAP published papers^4,5. The processing has four phases:

FPC project

For working with FPC^8,9, it is suggested you use release v5.0.8 from AGCoL.

1. It has the FPC demo files.
2. It has BLAT¹⁰ in the /ext directory.
3. It has the tar file doc.tar.gz of the documentation.
4. The AGCoL documentation applies to this release. See AGCoL System Guide.
5. This is the last release made from AGCoL, so the documentation will stay consistent.
6. It is also available from Github.

If you run into any problems, please do not hesitate to contact symap@agcol.arizona.edu.

References

¹ Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., Salzberg, S.L. (2004). Versatile and open software for comparing large genomes, Genome Biology, 5:R12

² Marcais, G., A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin (2018). MUMmer4: A fast and versatile genome alignment system, PLoS computational biology, 14(1): e1005944.

³ Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S. Jones, M. Marra (2009). Circos: An information aesthetic for comparative genomics. Genome Research doi:10.1101/gr.092759.109.

⁴ Soderlund, C., Nelson, W., Shoemaker, A., and Paterson, A.(2006). SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res. 16:1159-1168.

⁵ Soderlund, C., Bomhoff, M., and Nelson, W. (2011). SyMAP: A turnkey synteny system with application to multiple large duplicated plant sequenced genomes. Nucleic Acids Res V39, issue 10, e68.

⁶ Katoh, Standley (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772-780.

⁷ Edgar, R (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 113.

⁸ Soderlund, C., S. Humphrey, A. Dunhum, and L. French (2000). Contigs built with fingerprints, markers and FPC V4.7. Genome Research 10:1772-1787.

⁹ Engler, F., J. Hatfield, W. Nelson, and C. Soderlund (2003). Locating sequence on FPC maps and selecting a minimal tiling path. Genome Research 13:2152:2163.

¹⁰ Kent, J. (2002) BLAT--the BLAST-like alignment tool, Genome Research 12:656-64.

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Email Comments To: symap@agcol.arizona.edu