Search options:     ALFRED UID     Site name     Population name     Locus name/Official Gene Symbol Display options:     Samples typed for an individual site     Sample information     Sites typed for individual samples     Results in Google Earth     Area occupied by a population     Global populations Zooming and Panning Miscellaneous Helpful Tips Top Search Options: View Default ALFRED Map Interface Search with an ALFRED UID:View search box image • Filter map by (at the bottom left of the page); select what you are searching for (population, sample , site) from the pull down list • (1) Type in the complete ALFRED UID in the search box • Click the search button • (2) The site name will appear in green in the “Select ONE Site” box • (3) Click on “Display on Map”. View resulting image Search using a site name:View search box image • (1) Filter map by (at the bottom left of the page); select “site” from the pull down list • (2) Select the chromosome number on which the site is located • Select the locus in which the site is located from the pull down list • Click “Confirm Locus” • Select your site of interest from the pull down list (highlighted in green) • (3) Click “Display on Map” • Pie charts* are displayed on map. View resulting image OR • Filter map by (at the bottom left of the page); select “site” from the pull down list. View search box image • (1) Type the site name in the search box (you can also search using rs#, ss#, and GDB ID) • Click “Search” • (2) Select the desired site from the pull down list (will appear in green) • (3) Click “Display on Map” • Pie charts* are displayed on map *Pie charts displayed on the map display the average of the frequencies across all samples typed for that site Top Search using a population name: • Filter map by (at the bottom left of the page); select “population” from the pull down menuView search box image • (2) Click the “show all” box • Select the desired population from the pull down list • (3) Click “Display on Map”View resulting image OR • Filter map by (at the bottom left of the page); select “population” from the pull down listView search box image • (2) Type the population name in the search box (or a desired geographic region) • Click “Search” • Select the desired site from the pull down list (will appear in green) • (3) Click “Display on Map”View resulting image Search using locus name or Official Gene Symbol: • Filter map by (at the bottom left of the page); select “site” from the pull down list • (1) Type the locus name or the Official Gene Symbol in the search box • Click “Search” • (2) Select the desired site from the pull down list (will appear in green) • (3) Click “Display on Map” • Pie charts* are displayed on map *Pie charts displayed on the map display the average of the frequencies across all samples typed for that site. Top Display Options: To display the samples typed for an individual site: • See “Search using a site name” above in this help section, then; • Click on the center of a pie chart of the desired population • Population information will be display at the bottom of the pageView resulting table • Click on “View Charts”       o “Frequencies per sample of 10 globally most frequent alleles”: Pie charts will represent the allele frequencies for the top ten alleles found globally       o “Top 10 Allele Frequencies per Sample”: Pie charts represent the allele frequencies for the top ten alleles per sample • A separate window will open containing site information and the pie charts for all the samples (within the selected population) typed for that siteView resutling pie chart To display sample information: • Filter map by (at the bottom left of the page); select “sample” from the pull down list • (2) Click the “show all” box • Select the population to which the desired samples belong from the pull down list • (3) Click “Display on Map” • The population will be displayed on the map and all the samples (with their respective descriptions) will be listed in tabular format at the bottom of the page Top To display sites typed for individual samples: • Filter map by (at the bottom left of the page); select “sample” from the pull down list View search box image • (2) Click the “show all” box • Select the population to which the desired samples belong from the pull down list • (3) Click “Display on Map” • The population will be displayed on the map and all the samples (with their respective descriptions) will be listed in tabular format at the bottom of the page • Locate the desired sample • Click on “View Charts” • A separate window will open containing the pie charts and site information for all the sites typed for that sample View resulting image To display results in Google Earth**: • After retrieving the tabular results: • Check one or more of the boxes under the column “Display in Google Earth” for each population to be displayed in Google Earth. • Click the green “Show in Google Earth” button located under the map • Google Earth** will open displaying the rectangular area(s) occupied by the selected population(s) View resulting image       o When clicked, the icon at the center of each rectangle displays a callout containing the ALFRED population description along with a link to ALFRED for further informationView resulting image • **Google Earth is desktop software and must be installed before utilizing this particular function in ALFRED. Currently, this software is only available for Windows machines. To install Google Earth go to Google Top To display the area occupied by a population: • After retrieving the tabular results • Check one or more of the boxes under the column “Display Rectangular Area” • Click the green “Show Rectangular Area” button located under the map • A new window will open displaying the rectangular areas occupied by the selected population(s) View resulting image To view global populations: • Click “Global Populations” (located at the top right section of the page) • A separate window will open listing a number of populations found globally (because these populations are found globally they cannot be found on the map) To select a single population on the map: • Click on the triangle representing the population • The population information will be listed in tabular format on the bottom of the page Top Zooming and Panning: To zoom in/out on the map: • Click on “Zoom in” or “Zoom out” • Use the directions (N, S, E,W, etc.) along the sides of the map to re-center the map • To go back to the previous view, click “Go Back” Miscellaneous: To turn off population name labels: • Population name labels will be displayed with the corresponding pie charts • Click on “Toggle Population Name Display” box (located at the top of the page)View image • This may help view the pie charts unobstructed To select populations by drawing a rectangle around the desired area on the map: • Using the gold pull down menus located at the bottom of the map:View search box image • Select “Select by Rectangle” from the left gold pull down menu • Select how you want to accumulate your results from the right gold pull down menu:       o “Cumulative Results”: This option allows you to make multiple selections and the results to accumulate at the bottom of the page             • Each separate selection will be displayed as a different color       o“Individual Results”: This option will only allow you to display the results from ONE selection at the bottom of the page • Put your mouse pointer at the top left corner of the rectangle you want to draw • Click and drag the mouse down and to the right to create the rectangle View image • Populations selected will be listed in tabular format on the bottom of the page View search result Top To refresh/reset map: • Click “Reset view” located at the top of the map • This will clear the map along with any information retrieved To save the map as an image: Internet Explorer users • Right click on the map • Select “Save image as” or “Save picture as” • Name and save the image to your computer Netscape and Mozilla Firefox users • Right click on the map • Select “Save page as” • Name and save the file which has htm extension • 2 files will be saved.       o (1)folder with extension _files       o (2)file with extension .htm • The folder will have couple of image files. The image file which starts with ‘Alfred’ is the map image file. The legend to the map is also available from the same folder. To change the size of the pie chart: • Once the pie charts are displayed on the map look for the multi-colored pie chart (located off the upper right of the map) View image • Click “+” to increase the size of the pie or click “– “to decrease the size of the pie Top Helpful Tips: • When searching, make sure the filter mode is set (Site, Sample or Population) • Want more information? Links such as “More info” and “View ALFRED Site description” can be found throughout the map interface. Clicking on these links will take you to specific pages in ALFRED where more detailed information can be found. • Frequency pie charts display on map for individual sites can also be accessed from ‘Polymorphism Information’ page in ALFRED • Population location display on map can also be accessed from individual “Population Information’ page. Top of page

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© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan